1-241523216-A-G

Variant names:

• chr1-241523216-A-G
• rs1414493

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 0.624 in 151,728 control chromosomes in the GnomAD database, including 30,560 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 0.62 (30560 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94674 AN: 151610 Hom.: 30546 Cov.: 30

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.624 AC: 94722 AN: 151728 Hom.: 30560 Cov.: 30 AF XY: 0.627 AC XY: 46472 AN XY: 74168

African (AFR) AF: 0.467 AC: 19298 AN: 41360

American (AMR) AF: 0.614 AC: 9365 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2202 AN: 5138

South Asian (SAS) AF: 0.738 AC: 3550 AN: 4808

European-Finnish (FIN) AF: 0.742 AC: 7821 AN: 10542

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48100 AN: 67832

Other (OTH) AF: 0.609 AC: 1286 AN: 2110

Alfa AF: 0.660 Hom.: 12496

Bravo AF: 0.598

Asia WGS AF: 0.586 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1414493; hg19: chr1-241686516;