7-3878619-T-C

Variant names:

• chr7-3878619-T-C
• rs6958535
• NM_152744.4:c.847+57036T>C

Variant summary

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

The NM_152744.4(SDK1):​c.847+57036T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,182 control chromosomes in the GnomAD database, including 5,404 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 0.25 (5404 hom., cov: 33)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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.847+57036T>C		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.847+57036T>C		intron	N/A	ENSP00000385899.2	Q7Z5N4-1
	SDK1	ENST00000389531.7	TSL:5	c.847+57036T>C		intron	N/A	ENSP00000374182.3	F8W6X9

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38367 AN: 152064 Hom.: 5404 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.251

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.252 AC: 38412 AN: 152182 Hom.: 5404 Cov.: 33 AF XY: 0.249 AC XY: 18555 AN XY: 74402

African (AFR) AF: 0.381 AC: 15821 AN: 41496

American (AMR) AF: 0.235 AC: 3588 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.113 AC: 589 AN: 5192

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1592 AN: 10602

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13841 AN: 68000

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.220 Hom.: 15357

Bravo AF: 0.262

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.30
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs6958535; hg19: chr7-3918251;