1-67306899-A-G

Variant names:

• chr1-67306899-A-G
• rs3762317

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 0.225 in 152,034 control chromosomes in the GnomAD database, including 5,347 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 0.23 (5347 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.225 AC: 34198 AN: 151916 Hom.: 5330 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.225 AC: 34251 AN: 152034 Hom.: 5347 Cov.: 31 AF XY: 0.224 AC XY: 16649 AN XY: 74312

African (AFR) AF: 0.447 AC: 18521 AN: 41436

American (AMR) AF: 0.203 AC: 3103 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.156 AC: 811 AN: 5184

South Asian (SAS) AF: 0.157 AC: 755 AN: 4810

European-Finnish (FIN) AF: 0.133 AC: 1403 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8682 AN: 67976

Other (OTH) AF: 0.222 AC: 468 AN: 2108

Alfa AF: 0.166 Hom.: 1096

Bravo AF: 0.241

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		-0.51
PromoterAI		0.0035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3762317; hg19: chr1-67772582;