1-248832774-A-G

Variant names:

• chr1-248832774-A-G
• rs9727917

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 0.438 in 152,102 control chromosomes in the GnomAD database, including 16,386 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 0.44 (16386 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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: 0.438 AC: 66598 AN: 151984 Hom.: 16348 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.438 AC: 66693 AN: 152102 Hom.: 16386 Cov.: 33 AF XY: 0.444 AC XY: 33006 AN XY: 74366

African (AFR) AF: 0.666 AC: 27631 AN: 41486

American (AMR) AF: 0.419 AC: 6398 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1227 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2725 AN: 5180

South Asian (SAS) AF: 0.513 AC: 2473 AN: 4822

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10566

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21302 AN: 67988

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.345 Hom.: 15827

Bravo AF: 0.459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.50
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs9727917; hg19: chr1-249126973;