NM_152744.4:c.3203-718G>A

Variant names:

• chr7-4078745-G-A
• rs34912216
• NM_152744.4:c.3203-718G>A

Variant summary

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

The NM_152744.4(SDK1):​c.3203-718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,082 control chromosomes in the GnomAD database, including 12,395 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 0.36 (12395 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK1	NM_152744.4	c.3203-718G>A		intron_variant	Intron 21 of 44	ENST00000404826.7	NP_689957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDK1	ENST00000404826.7	c.3203-718G>A		intron_variant	Intron 21 of 44	1	NM_152744.4	ENSP00000385899.2
SDK1	ENST00000389531.7	c.3203-718G>A		intron_variant	Intron 21 of 43	5		ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55442 AN: 151964 Hom.: 12380 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.365 AC: 55499 AN: 152082 Hom.: 12395 Cov.: 32 AF XY: 0.358 AC XY: 26606 AN XY: 74346

African (AFR) AF: 0.633 AC: 26238 AN: 41468

American (AMR) AF: 0.241 AC: 3680 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3470

East Asian (EAS) AF: 0.0672 AC: 347 AN: 5162

South Asian (SAS) AF: 0.334 AC: 1607 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2500 AN: 10592

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19094 AN: 67978

Other (OTH) AF: 0.322 AC: 681 AN: 2112

Alfa AF: 0.338 Hom.: 4327

Bravo AF: 0.373

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.65
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs34912216; hg19: chr7-4118377;