rs6747506

Variant names:

• chr2-73294754-A-T
• rs6747506

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 0.235 in 151,780 control chromosomes in the GnomAD database, including 7,873 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 0.23 (7873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.234 AC: 35536 AN: 151662 Hom.: 7835 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.235 AC: 35637 AN: 151780 Hom.: 7873 Cov.: 32 AF XY: 0.235 AC XY: 17464 AN XY: 74188

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.206

Alfa AF: 0.157 Hom.: 613

Bravo AF: 0.265

Asia WGS AF: 0.341 AC: 1185 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	9.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6747506; hg19: chr2-73521882;