rs4837656

Variant names:

• chr9-119671775-T-C
• rs4837656
• ENST00000750211.1:n.498-52909A>G

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.498-52909A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,946 control chromosomes in the GnomAD database, including 5,798 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 0.27 (5798 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 2 publications found

Genes affected

ENSG00000297691 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.297 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
ENSG00000297691	ENST00000750211.1	n.498-52909A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40553 AN: 151828 Hom.: 5785 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.267 AC: 40612 AN: 151946 Hom.: 5798 Cov.: 32 AF XY: 0.266 AC XY: 19759 AN XY: 74260

African (AFR) AF: 0.236 AC: 9797 AN: 41444

American (AMR) AF: 0.247 AC: 3774 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3468

East Asian (EAS) AF: 0.0248 AC: 128 AN: 5170

South Asian (SAS) AF: 0.108 AC: 519 AN: 4812

European-Finnish (FIN) AF: 0.402 AC: 4238 AN: 10532

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20442 AN: 67942

Other (OTH) AF: 0.258 AC: 543 AN: 2106

Alfa AF: 0.285 Hom.: 26955

Bravo AF: 0.256

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4837656; hg19: chr9-122434053; COSMIC: COSV60399620;