chr1-160111579-G-A

Variant names:

• chr1-160111579-G-A
• rs11800782

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0302 in 152,290 control chromosomes in the GnomAD database, including 102 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 0.030 (102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0302 (4605/152290) while in subpopulation NFE AF = 0.044 (2995/68010). AF 95% confidence interval is 0.0427. There are 102 homozygotes in GnomAd4. There are 2224 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 102 gene

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: 0.0303 AC: 4607 AN: 152174 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.00743

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0302 AC: 4605 AN: 152290 Hom.: 102 Cov.: 32 AF XY: 0.0299 AC XY: 2224 AN XY: 74478

African (AFR) AF: 0.00741 AC: 308 AN: 41586

American (AMR) AF: 0.0381 AC: 583 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00994 AC: 48 AN: 4830

European-Finnish (FIN) AF: 0.0356 AC: 376 AN: 10574

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2995 AN: 68010

Other (OTH) AF: 0.0412 AC: 87 AN: 2114

Alfa AF: 0.0391 Hom.: 69

Bravo AF: 0.0307

Asia WGS AF: 0.00577 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs11800782; hg19: chr1-160081369;