chr1-162060117-A-T

Position:

• chr1-162060117-A-T

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 0.477 in 152,124 control chromosomes in the GnomAD database, including 21,496 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 0.48 (21496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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: 0.477 AC: 72548 AN: 152006 Hom.: 21480 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.477 AC: 72577 AN: 152124 Hom.: 21496 Cov.: 32 AF XY: 0.477 AC XY: 35448 AN XY: 74368

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.516

Alfa AF: 0.566 Hom.: 3411

Bravo AF: 0.464

Asia WGS AF: 0.302 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4657139; hg19: chr1-162029907;