1-162051179-T-A

Variant names:

• chr1-162051179-T-A
• rs7539120

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 0.544 in 145,112 control chromosomes in the GnomAD database, including 22,070 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 0.54 (22070 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.544 AC: 78976 AN: 145116 Hom.: 22063 Cov.: 25

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.544 AC: 78988 AN: 145112 Hom.: 22070 Cov.: 25 AF XY: 0.539 AC XY: 37956 AN XY: 70422

African (AFR) AF: 0.479 AC: 18964 AN: 39614

American (AMR) AF: 0.569 AC: 8219 AN: 14456

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1897 AN: 3434

East Asian (EAS) AF: 0.277 AC: 1392 AN: 5022

South Asian (SAS) AF: 0.321 AC: 1488 AN: 4638

European-Finnish (FIN) AF: 0.572 AC: 4600 AN: 8040

Middle Eastern (MID) AF: 0.594 AC: 165 AN: 278

European-Non Finnish (NFE) AF: 0.609 AC: 40613 AN: 66716

Other (OTH) AF: 0.558 AC: 1120 AN: 2008

Alfa AF: 0.402 Hom.: 843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.18
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7539120; hg19: chr1-162020969;