rs1859121

Variant names:

• chr7-95347655-T-C
• rs1859121

Your query was ambiguous. Multiple possible variants found:

• chr7-95347655-T-C
• chr7-95347655-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 0.544 in 151,962 control chromosomes in the GnomAD database, including 23,043 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 0.54 (23043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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: 0.543 AC: 82527 AN: 151844 Hom.: 22990 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.544 AC: 82638 AN: 151962 Hom.: 23043 Cov.: 32 AF XY: 0.558 AC XY: 41409 AN XY: 74248

African (AFR) AF: 0.582 AC: 24126 AN: 41422

American (AMR) AF: 0.614 AC: 9376 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3468

East Asian (EAS) AF: 0.781 AC: 4032 AN: 5160

South Asian (SAS) AF: 0.691 AC: 3330 AN: 4820

European-Finnish (FIN) AF: 0.626 AC: 6605 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31928 AN: 67948

Other (OTH) AF: 0.521 AC: 1102 AN: 2114

Alfa AF: 0.493 Hom.: 31507

Bravo AF: 0.544

Asia WGS AF: 0.738 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.68
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1859121; hg19: chr7-94976967;