2-67971235-G-T

Position:

• chr2-67971235-G-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.67971235G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.728

Alfa AF: 0.752 Hom.: 71366

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12713624; hg19: chr2-68198367;