rs1859646

Variant names:

• chr7-141795804-G-A
• rs1859646

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 0.479 in 151,894 control chromosomes in the GnomAD database, including 17,812 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 0.48 (17812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.479 AC: 72754 AN: 151776 Hom.: 17783 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.479 AC: 72832 AN: 151894 Hom.: 17812 Cov.: 32 AF XY: 0.484 AC XY: 35910 AN XY: 74222

African (AFR) AF: 0.387 AC: 16036 AN: 41410

American (AMR) AF: 0.535 AC: 8165 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3466

East Asian (EAS) AF: 0.757 AC: 3904 AN: 5158

South Asian (SAS) AF: 0.593 AC: 2854 AN: 4810

European-Finnish (FIN) AF: 0.484 AC: 5099 AN: 10534

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33728 AN: 67942

Other (OTH) AF: 0.493 AC: 1040 AN: 2108

Alfa AF: 0.497 Hom.: 21138

Bravo AF: 0.481

Asia WGS AF: 0.671 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.22
DANN	Benign	0.23
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1859646; hg19: chr7-141495604;