NM_152744.4:c.848-54649T>C

Variant names:

• chr7-3896274-T-C
• rs6959674
• NM_152744.4:c.848-54649T>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.848-54649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,228 control chromosomes in the GnomAD database, including 7,123 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 0.28 (7123 hom., cov: 33)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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.848-54649T>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.848-54649T>C		intron	N/A	ENSP00000385899.2
	SDK1	ENST00000389531.7	TSL:5	c.848-54649T>C		intron	N/A	ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42976 AN: 152110 Hom.: 7111 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.283 AC: 43039 AN: 152228 Hom.: 7123 Cov.: 33 AF XY: 0.280 AC XY: 20827 AN XY: 74446

African (AFR) AF: 0.464 AC: 19253 AN: 41508

American (AMR) AF: 0.273 AC: 4182 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3466

East Asian (EAS) AF: 0.114 AC: 591 AN: 5180

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4818

European-Finnish (FIN) AF: 0.153 AC: 1621 AN: 10618

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14335 AN: 68020

Other (OTH) AF: 0.294 AC: 622 AN: 2116

Alfa AF: 0.169 Hom.: 484

Bravo AF: 0.297

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.70
PhyloP100		-0.79
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: rs6959674; hg19: chr7-3935906;