rs1174864

Variant names:

• chr7-53059866-G-A
• rs1174864

Your query was ambiguous. Multiple possible variants found:

• chr7-53059866-G-A
• chr7-53059866-G-C
• chr7-53059866-G-T

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 0.511 in 152,054 control chromosomes in the GnomAD database, including 20,369 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 0.51 (20369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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: 0.511 AC: 77577 AN: 151936 Hom.: 20364 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.511 AC: 77627 AN: 152054 Hom.: 20369 Cov.: 32 AF XY: 0.507 AC XY: 37660 AN XY: 74296

African (AFR) AF: 0.495 AC: 20512 AN: 41468

American (AMR) AF: 0.510 AC: 7799 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1818 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1002 AN: 5150

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4818

European-Finnish (FIN) AF: 0.608 AC: 6425 AN: 10566

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36885 AN: 67986

Other (OTH) AF: 0.538 AC: 1137 AN: 2112

Alfa AF: 0.527 Hom.: 41267

Bravo AF: 0.502

Asia WGS AF: 0.294 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.69
DANN	Benign	0.54
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs1174864; hg19: chr7-53127559;