chr1-205079255-T-C

Variant names:

• chr1-205079255-T-C
• rs7523477

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 0.799 in 152,126 control chromosomes in the GnomAD database, including 49,816 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 0.80 (49816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 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: 0.800 AC: 121560 AN: 152008 Hom.: 49800 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.799 AC: 121616 AN: 152126 Hom.: 49816 Cov.: 32 AF XY: 0.803 AC XY: 59736 AN XY: 74370

African (AFR) AF: 0.598 AC: 24770 AN: 41452

American (AMR) AF: 0.880 AC: 13462 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3470

East Asian (EAS) AF: 0.970 AC: 5009 AN: 5166

South Asian (SAS) AF: 0.913 AC: 4398 AN: 4818

European-Finnish (FIN) AF: 0.889 AC: 9415 AN: 10594

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58686 AN: 68008

Other (OTH) AF: 0.843 AC: 1783 AN: 2116

Alfa AF: 0.854 Hom.: 86356

Bravo AF: 0.793

Asia WGS AF: 0.928 AC: 3228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7523477; hg19: chr1-205048383;