7-4030792-C-T

Variant names:

• chr7-4030792-C-T
• rs2880371
• NM_152744.4:c.2602+13440C>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.2602+13440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,092 control chromosomes in the GnomAD database, including 9,621 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 0.29 (9621 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.844
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK1	NM_152744.4	c.2602+13440C>T		intron_variant	Intron 17 of 44	ENST00000404826.7	NP_689957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDK1	ENST00000404826.7	c.2602+13440C>T		intron_variant	Intron 17 of 44	1	NM_152744.4	ENSP00000385899.2
SDK1	ENST00000389531.7	c.2602+13440C>T		intron_variant	Intron 17 of 43	5		ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44339 AN: 151974 Hom.: 9579 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.292 AC: 44444 AN: 152092 Hom.: 9621 Cov.: 32 AF XY: 0.289 AC XY: 21489 AN XY: 74346

African (AFR) AF: 0.614 AC: 25469 AN: 41460

American (AMR) AF: 0.203 AC: 3102 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3470

East Asian (EAS) AF: 0.0744 AC: 385 AN: 5176

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1729 AN: 10568

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11533 AN: 68006

Other (OTH) AF: 0.252 AC: 532 AN: 2110

Alfa AF: 0.177 Hom.: 1633

Bravo AF: 0.308

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.48
PhyloP100		0.84
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: rs2880371; hg19: chr7-4070424;