1-242788776-T-G

Variant names:

• chr1-242788776-T-G
• rs914951

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 0.618 in 151,992 control chromosomes in the GnomAD database, including 29,286 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 (29286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.618 AC: 93813 AN: 151874 Hom.: 29256 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.618 AC: 93903 AN: 151992 Hom.: 29286 Cov.: 32 AF XY: 0.623 AC XY: 46239 AN XY: 74270

African (AFR) AF: 0.577 AC: 23908 AN: 41458

American (AMR) AF: 0.637 AC: 9727 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1861 AN: 3466

East Asian (EAS) AF: 0.846 AC: 4374 AN: 5170

South Asian (SAS) AF: 0.789 AC: 3794 AN: 4810

European-Finnish (FIN) AF: 0.618 AC: 6514 AN: 10544

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.614 AC: 41755 AN: 67966

Other (OTH) AF: 0.622 AC: 1313 AN: 2112

Alfa AF: 0.602 Hom.: 31247

Bravo AF: 0.609

Asia WGS AF: 0.823 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs914951; hg19: chr1-242952078;