chr1-64402669-G-A

Variant names:

• chr1-64402669-G-A
• rs11208446

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 0.152 in 151,988 control chromosomes in the GnomAD database, including 2,334 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 0.15 (2334 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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: 0.152 AC: 23108 AN: 151870 Hom.: 2327 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.152 AC: 23135 AN: 151988 Hom.: 2334 Cov.: 31 AF XY: 0.154 AC XY: 11404 AN XY: 74290

African (AFR) AF: 0.286 AC: 11866 AN: 41442

American (AMR) AF: 0.0764 AC: 1167 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3470

East Asian (EAS) AF: 0.0825 AC: 426 AN: 5166

South Asian (SAS) AF: 0.147 AC: 706 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2047 AN: 10548

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

European-Non Finnish (NFE) AF: 0.0937 AC: 6366 AN: 67954

Other (OTH) AF: 0.119 AC: 251 AN: 2110

Alfa AF: 0.107 Hom.: 3839

Bravo AF: 0.148

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.39
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11208446; hg19: chr1-64868352;