7-3875932-T-C

Variant names:

• chr7-3875932-T-C
• rs6462411
• NM_152744.4:c.847+54349T>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+54349T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,096 control chromosomes in the GnomAD database, including 11,134 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 0.33 (11134 hom., cov: 33)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 12 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	NM_152744.4	MANE Select	c.847+54349T>C		intron	N/A	NP_689957.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	ENST00000404826.7	TSL:1 MANE Select	c.847+54349T>C		intron	N/A	ENSP00000385899.2
	SDK1	ENST00000389531.7	TSL:5	c.847+54349T>C		intron	N/A	ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49919 AN: 151978 Hom.: 11097 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.329 AC: 50015 AN: 152096 Hom.: 11134 Cov.: 33 AF XY: 0.324 AC XY: 24072 AN XY: 74358

African (AFR) AF: 0.638 AC: 26456 AN: 41460

American (AMR) AF: 0.277 AC: 4227 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5170

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4816

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

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13940 AN: 67990

Other (OTH) AF: 0.316 AC: 662 AN: 2098

Alfa AF: 0.242 Hom.: 19078

Bravo AF: 0.349

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.50
PhyloP100		-1.0
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: rs6462411; hg19: chr7-3915564;