1-234983635-G-T

Variant names:

• chr1-234983635-G-T
• rs6586361

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 0.514 in 152,066 control chromosomes in the GnomAD database, including 21,283 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 (21283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.514 AC: 78066 AN: 151948 Hom.: 21249 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.514 AC: 78150 AN: 152066 Hom.: 21283 Cov.: 32 AF XY: 0.503 AC XY: 37380 AN XY: 74328

African (AFR) AF: 0.687 AC: 28513 AN: 41478

American (AMR) AF: 0.358 AC: 5478 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1063 AN: 5178

South Asian (SAS) AF: 0.442 AC: 2133 AN: 4824

European-Finnish (FIN) AF: 0.411 AC: 4349 AN: 10570

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32951 AN: 67952

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

Alfa AF: 0.483 Hom.: 75026

Bravo AF: 0.514

Asia WGS AF: 0.350 AC: 1216 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs6586361; hg19: chr1-235119382; COSMIC: COSV73420344;