rs7565981

Variant names:

• chr2-100807869-G-A
• rs7565981

Your query was ambiguous. Multiple possible variants found:

• chr2-100807869-G-A
• chr2-100807869-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 0.148 in 152,090 control chromosomes in the GnomAD database, including 2,693 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 0.15 (2693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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: 0.148 AC: 22434 AN: 151970 Hom.: 2679 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.148 AC: 22477 AN: 152090 Hom.: 2693 Cov.: 32 AF XY: 0.149 AC XY: 11110 AN XY: 74352

African (AFR) AF: 0.277 AC: 11475 AN: 41418

American (AMR) AF: 0.122 AC: 1871 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2648 AN: 5148

South Asian (SAS) AF: 0.151 AC: 732 AN: 4832

European-Finnish (FIN) AF: 0.0784 AC: 831 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4084 AN: 68012

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.0993 Hom.: 3798

Bravo AF: 0.160

Asia WGS AF: 0.329 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs7565981; hg19: chr2-101424331;