chr6-45729051-A-G

Variant names:

• chr6-45729051-A-G
• rs1932040

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 0.693 in 152,086 control chromosomes in the GnomAD database, including 38,288 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 0.69 (38288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.694 AC: 105445 AN: 151966 Hom.: 38303 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.693 AC: 105444 AN: 152086 Hom.: 38288 Cov.: 32 AF XY: 0.688 AC XY: 51115 AN XY: 74344

African (AFR) AF: 0.502 AC: 20819 AN: 41434

American (AMR) AF: 0.635 AC: 9711 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3021 AN: 3472

East Asian (EAS) AF: 0.367 AC: 1898 AN: 5168

South Asian (SAS) AF: 0.829 AC: 4003 AN: 4828

European-Finnish (FIN) AF: 0.739 AC: 7819 AN: 10580

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55708 AN: 68002

Other (OTH) AF: 0.710 AC: 1497 AN: 2108

Alfa AF: 0.744 Hom.: 5367

Bravo AF: 0.675

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.52
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs1932040; hg19: chr6-45696788;