rs6751663

Positions:

• chr2-67960000-C-G
• chr2-67960000-C-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 0.519 in 151,858 control chromosomes in the GnomAD database, including 20,755 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 0.52 (20755 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67960000C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78702 AN: 151740 Hom.: 20734 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.519 AC: 78771 AN: 151858 Hom.: 20755 Cov.: 31 AF XY: 0.513 AC XY: 38079 AN XY: 74206

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.514

Alfa AF: 0.394 Hom.: 1009

Bravo AF: 0.524

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6751663; hg19: chr2-68187132;