chr2-84137812-G-C

Variant names:

• chr2-84137812-G-C
• rs10496306

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 0.194 in 152,164 control chromosomes in the GnomAD database, including 3,179 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 0.19 (3179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 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: 0.194 AC: 29571 AN: 152044 Hom.: 3180 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.194 AC: 29575 AN: 152164 Hom.: 3179 Cov.: 32 AF XY: 0.195 AC XY: 14475 AN XY: 74390

African (AFR) AF: 0.117 AC: 4856 AN: 41532

American (AMR) AF: 0.199 AC: 3044 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3472

East Asian (EAS) AF: 0.0870 AC: 450 AN: 5174

South Asian (SAS) AF: 0.129 AC: 624 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2442 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16323 AN: 67992

Other (OTH) AF: 0.223 AC: 471 AN: 2112

Alfa AF: 0.226 Hom.: 487

Bravo AF: 0.190

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10496306; hg19: chr2-84364936;