1-91479340-G-C

Variant names:

• chr1-91479340-G-C
• rs6604023

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 0.254 in 151,392 control chromosomes in the GnomAD database, including 5,783 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 0.25 (5783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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: 0.254 AC: 38362 AN: 151278 Hom.: 5776 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.254 AC: 38405 AN: 151392 Hom.: 5783 Cov.: 31 AF XY: 0.259 AC XY: 19132 AN XY: 74008

African (AFR) AF: 0.409 AC: 16695 AN: 40866

American (AMR) AF: 0.302 AC: 4603 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3468

East Asian (EAS) AF: 0.131 AC: 674 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1143 AN: 4804

European-Finnish (FIN) AF: 0.268 AC: 2838 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11238 AN: 67964

Other (OTH) AF: 0.234 AC: 492 AN: 2106

Alfa AF: 0.102 Hom.: 164

Bravo AF: 0.260

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.77
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs6604023; hg19: chr1-91944897;