1-64695547-T-G

Variant names:

• chr1-64695547-T-G
• rs1926304

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 0.272 in 152,014 control chromosomes in the GnomAD database, including 7,060 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 0.27 (7060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.272 AC: 41316 AN: 151894 Hom.: 7046 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.272 AC: 41375 AN: 152014 Hom.: 7060 Cov.: 32 AF XY: 0.278 AC XY: 20657 AN XY: 74288

African (AFR) AF: 0.411 AC: 17041 AN: 41450

American (AMR) AF: 0.313 AC: 4789 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3442 AN: 5160

South Asian (SAS) AF: 0.278 AC: 1336 AN: 4812

European-Finnish (FIN) AF: 0.254 AC: 2685 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10651 AN: 67966

Other (OTH) AF: 0.265 AC: 560 AN: 2110

Alfa AF: 0.196 Hom.: 14809

Bravo AF: 0.292

Asia WGS AF: 0.479 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs1926304; hg19: chr1-65161230;