rs2181107

Variant names:

• chr6-269735-G-A
• rs2181107

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.0378 in 151,180 control chromosomes in the GnomAD database, including 65 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 0.038 (65 hom., cov: 52)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS2: High Homozygotes in GnomAd4 at 65 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: 0.0378 AC: 5713 AN: 151068 Hom.: 64 Cov.: 52

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.00641

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00711

Gnomad OTH AF: 0.0366

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

GnomAD4 genome AF: 0.0378 AC: 5720 AN: 151180 Hom.: 65 Cov.: 52 AF XY: 0.0407 AC XY: 3007 AN XY: 73912

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0564 AC: 2307 AN: 40878

American (AMR) AF: 0.100 AC: 1513 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1017 AN: 5064

South Asian (SAS) AF: 0.0481 AC: 229 AN: 4764

European-Finnish (FIN) AF: 0.00641 AC: 68 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00712 AC: 484 AN: 67962

Other (OTH) AF: 0.0363 AC: 76 AN: 2096

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0355 Hom.: 35

Asia WGS AF: 0.129 AC: 450 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2181107; hg19: chr6-269735;