chr2-102417980-T-C

Variant names:

• chr2-102417980-T-C
• rs11465670

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 0.131 in 152,288 control chromosomes in the GnomAD database, including 1,454 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 0.13 (1454 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.130 AC: 19858 AN: 152170 Hom.: 1448 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.131 AC: 19883 AN: 152288 Hom.: 1454 Cov.: 33 AF XY: 0.127 AC XY: 9466 AN XY: 74474

African (AFR) AF: 0.178 AC: 7388 AN: 41530

American (AMR) AF: 0.0972 AC: 1488 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5192

South Asian (SAS) AF: 0.0918 AC: 444 AN: 4834

European-Finnish (FIN) AF: 0.0888 AC: 943 AN: 10618

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8702 AN: 68022

Other (OTH) AF: 0.118 AC: 250 AN: 2112

Alfa AF: 0.127 Hom.: 1666

Bravo AF: 0.135

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.81
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs11465670; hg19: chr2-103034440;