chr2-96111592-C-T

Variant names:

• chr2-96111592-C-T
• rs7604842

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 0.665 in 152,150 control chromosomes in the GnomAD database, including 34,378 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 0.67 (34378 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.745 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: 0.666 AC: 101179 AN: 152032 Hom.: 34372 Cov.: 33

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.665 AC: 101223 AN: 152150 Hom.: 34378 Cov.: 33 AF XY: 0.660 AC XY: 49093 AN XY: 74364

African (AFR) AF: 0.732 AC: 30377 AN: 41508

American (AMR) AF: 0.595 AC: 9106 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2100 AN: 5174

South Asian (SAS) AF: 0.766 AC: 3689 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5570 AN: 10574

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45358 AN: 68002

Other (OTH) AF: 0.710 AC: 1500 AN: 2112

Alfa AF: 0.664 Hom.: 11844

Bravo AF: 0.662

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.3
DANN	Benign	0.20
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7604842; hg19: chr2-96777340;