chr2-67971235-G-T

Variant names:

• chr2-67971235-G-T
• rs12713624

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 0.717 in 152,106 control chromosomes in the GnomAD database, including 39,262 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 0.72 (39262 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 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: 0.717 AC: 108942 AN: 151988 Hom.: 39246 Cov.: 34

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.717 AC: 109002 AN: 152106 Hom.: 39262 Cov.: 34 AF XY: 0.716 AC XY: 53201 AN XY: 74342

African (AFR) AF: 0.638 AC: 26461 AN: 41480

American (AMR) AF: 0.752 AC: 11494 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2441 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3562 AN: 5170

South Asian (SAS) AF: 0.702 AC: 3387 AN: 4828

European-Finnish (FIN) AF: 0.726 AC: 7688 AN: 10586

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51588 AN: 67978

Other (OTH) AF: 0.728 AC: 1539 AN: 2114

Alfa AF: 0.744 Hom.: 113926

Bravo AF: 0.715

Asia WGS AF: 0.708 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.70
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12713624; hg19: chr2-68198367;