1-169508336-A-C

Position:

• chr1-169508336-A-C

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 0.927 in 152,184 control chromosomes in the GnomAD database, including 65,391 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 0.93 (65391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.927 AC: 140905 AN: 152066 Hom.: 65334 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.927 AC: 141021 AN: 152184 Hom.: 65391 Cov.: 32 AF XY: 0.928 AC XY: 69072 AN XY: 74402

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.925

Alfa AF: 0.930 Hom.: 78416

Bravo AF: 0.925

Asia WGS AF: 0.973 AC: 3385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6687813; hg19: chr1-169477574;