rs7565981

Positions:

• chr2-100807869-G-A
• chr2-100807869-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0784

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.161

Alfa AF: 0.0845 Hom.: 498

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7565981; hg19: chr2-101424331;