NM_152744.4:c.1817+131C>T

Variant names:

• chr7-3971699-C-T
• rs6965800
• NM_152744.4:c.1817+131C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152744.4(SDK1):​c.1817+131C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 701,110 control chromosomes in the GnomAD database, including 46,581 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (15355 hom., cov: 32)
  • Exomes 𝑓: 0.33 (31226 hom.)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 3 publications found

Genes affected

SDK1 (HGNC:19307): (sidekick cell adhesion molecule 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152744.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	NM_152744.4	MANE Select	c.1817+131C>T		intron	N/A	NP_689957.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	ENST00000404826.7	TSL:1 MANE Select	c.1817+131C>T		intron	N/A	ENSP00000385899.2	Q7Z5N4-1
	SDK1	ENST00000389531.7	TSL:5	c.1817+131C>T		intron	N/A	ENSP00000374182.3	F8W6X9
	SDK1	ENST00000484011.1	TSL:3	n.103+131C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63527 AN: 151994 Hom.: 15317 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.397

GnomAD4 exome AF: 0.326 AC: 178968 AN: 548998 Hom.: 31226 AF XY: 0.325 AC XY: 93947 AN XY: 289294

African (AFR) AF: 0.674 AC: 10503 AN: 15576

American (AMR) AF: 0.411 AC: 13288 AN: 32334

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 6634 AN: 17992

East Asian (EAS) AF: 0.167 AC: 5286 AN: 31580

South Asian (SAS) AF: 0.327 AC: 18413 AN: 56250

European-Finnish (FIN) AF: 0.321 AC: 11373 AN: 35412

Middle Eastern (MID) AF: 0.370 AC: 1047 AN: 2826

European-Non Finnish (NFE) AF: 0.313 AC: 102299 AN: 327118

Other (OTH) AF: 0.339 AC: 10125 AN: 29910

GnomAD4 genome AF: 0.418 AC: 63620 AN: 152112 Hom.: 15355 Cov.: 32 AF XY: 0.415 AC XY: 30867 AN XY: 74354

African (AFR) AF: 0.674 AC: 27981 AN: 41492

American (AMR) AF: 0.388 AC: 5940 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3468

East Asian (EAS) AF: 0.174 AC: 898 AN: 5168

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3533 AN: 10576

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21260 AN: 67980

Other (OTH) AF: 0.398 AC: 839 AN: 2110

Alfa AF: 0.375 Hom.: 4686

Bravo AF: 0.434

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6965800; hg19: chr7-4011331;