1-247838264-G-A

Position:

• chr1-247838264-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.139 in 152,154 control chromosomes in the GnomAD database, including 2,787 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 0.14 (2787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

ACMG classification

Verdict is Benign. Variant got -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 = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21047 AN: 152036 Hom.: 2775 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.139 AC: 21103 AN: 152154 Hom.: 2787 Cov.: 32 AF XY: 0.135 AC XY: 10019 AN XY: 74400

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00637

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.0226

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0787 Hom.: 447

Bravo AF: 0.151

Asia WGS AF: 0.0520 AC: 180 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	3.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7512555; hg19: chr1-248001566;