NM_152744.4:c.713+61818A>G

Variant names:

• chr7-3703923-A-G
• rs10256504
• NM_152744.4:c.713+61818A>G

Variant summary

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

The NM_152744.4(SDK1):​c.713+61818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,140 control chromosomes in the GnomAD database, including 1,275 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 0.12 (1275 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 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.713+61818A>G		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.713+61818A>G		intron	N/A	ENSP00000385899.2	Q7Z5N4-1
	SDK1	ENST00000389531.7	TSL:5	c.713+61818A>G		intron	N/A	ENSP00000374182.3	F8W6X9

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18396 AN: 152022 Hom.: 1271 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.121 AC: 18426 AN: 152140 Hom.: 1275 Cov.: 32 AF XY: 0.121 AC XY: 9031 AN XY: 74388

African (AFR) AF: 0.157 AC: 6505 AN: 41486

American (AMR) AF: 0.160 AC: 2440 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3472

East Asian (EAS) AF: 0.0638 AC: 330 AN: 5174

South Asian (SAS) AF: 0.196 AC: 947 AN: 4828

European-Finnish (FIN) AF: 0.0731 AC: 774 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6410 AN: 67988

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.109 Hom.: 1399

Bravo AF: 0.129

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.30
PhyloP100		0.24
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: rs10256504; hg19: chr7-3743555;