rs6746896

Variant names:

• chr2-96745212-A-G
• rs6746896

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 0.256 in 151,952 control chromosomes in the GnomAD database, including 5,985 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 0.26 (5985 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 47 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 = 0.32 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: 0.257 AC: 38967 AN: 151834 Hom.: 5992 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.256 AC: 38962 AN: 151952 Hom.: 5985 Cov.: 31 AF XY: 0.260 AC XY: 19313 AN XY: 74234

African (AFR) AF: 0.122 AC: 5047 AN: 41486

American (AMR) AF: 0.197 AC: 3002 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1669 AN: 5158

South Asian (SAS) AF: 0.182 AC: 877 AN: 4806

European-Finnish (FIN) AF: 0.471 AC: 4955 AN: 10528

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21955 AN: 67944

Other (OTH) AF: 0.207 AC: 438 AN: 2112

Alfa AF: 0.295 Hom.: 20849

Bravo AF: 0.232

Asia WGS AF: 0.257 AC: 894 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	1.6
DANN	Benign	0.57
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs6746896; hg19: chr2-97410949;