rs1910739

Variant names:

• chr4-51817441-T-C
• rs1910739

Your query was ambiguous. Multiple possible variants found:

• chr4-51817441-T-C
• chr4-51817441-T-G

Variant summary

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

The variant allele was found at a frequency of 0.366 in 151,892 control chromosomes in the GnomAD database, including 11,876 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 0.37 (11876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 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

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55535 AN: 151774 Hom.: 11876 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.366 AC: 55569 AN: 151892 Hom.: 11876 Cov.: 32 AF XY: 0.369 AC XY: 27381 AN XY: 74224

African (AFR) AF: 0.575 AC: 23805 AN: 41412

American (AMR) AF: 0.266 AC: 4040 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3468

East Asian (EAS) AF: 0.612 AC: 3141 AN: 5136

South Asian (SAS) AF: 0.459 AC: 2216 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3195 AN: 10560

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

European-Non Finnish (NFE) AF: 0.258 AC: 17521 AN: 67978

Other (OTH) AF: 0.301 AC: 634 AN: 2108

Alfa AF: 0.295 Hom.: 13763

Bravo AF: 0.368

Asia WGS AF: 0.503 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.26
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1910739; hg19: chr4-52683607;