rs957749

Variant names:

• chr2-210755857-A-G
• rs957749
• ENST00000737540.1:n.436-2491A>G

Variant summary

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

The ENST00000737540.1(ENSG00000296241):​n.436-2491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,910 control chromosomes in the GnomAD database, including 5,271 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 0.26 (5271 hom., cov: 32)
• Consequence: ENSG00000296241 ENST00000737540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 3 publications found

Genes affected

ENSG00000296241 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296241	ENST00000737540.1	n.436-2491A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39280 AN: 151790 Hom.: 5266 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.259 AC: 39307 AN: 151910 Hom.: 5271 Cov.: 32 AF XY: 0.255 AC XY: 18938 AN XY: 74220

African (AFR) AF: 0.214 AC: 8857 AN: 41474

American (AMR) AF: 0.256 AC: 3901 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5168

South Asian (SAS) AF: 0.333 AC: 1600 AN: 4810

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20312 AN: 67870

Other (OTH) AF: 0.276 AC: 582 AN: 2110

Alfa AF: 0.287 Hom.: 3437

Bravo AF: 0.258

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		0.0090

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs957749; hg19: chr2-211620581;