rs1106683

Variant names:

• chr7-131768766-G-A
• rs1106683

Your query was ambiguous. Multiple possible variants found:

• chr7-131768766-G-A
• chr7-131768766-G-C

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 0.143 in 152,218 control chromosomes in the GnomAD database, including 1,634 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 0.14 (1634 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

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: 0.143 AC: 21741 AN: 152100 Hom.: 1635 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.143 AC: 21755 AN: 152218 Hom.: 1634 Cov.: 33 AF XY: 0.144 AC XY: 10681 AN XY: 74410

African (AFR) AF: 0.156 AC: 6486 AN: 41556

American (AMR) AF: 0.103 AC: 1568 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3472

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5180

South Asian (SAS) AF: 0.109 AC: 523 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2038 AN: 10582

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9956 AN: 67994

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.137 Hom.: 4028

Bravo AF: 0.135

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.93
DANN	Benign	0.47
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs1106683; hg19: chr7-131453525;