rs2738046

Variant names:

• chr8-6966020-C-A
• rs2738046

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 0.481 in 151,986 control chromosomes in the GnomAD database, including 17,750 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 0.48 (17750 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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: 0.481 AC: 73049 AN: 151868 Hom.: 17705 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.481 AC: 73149 AN: 151986 Hom.: 17750 Cov.: 32 AF XY: 0.485 AC XY: 36024 AN XY: 74292

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.458

Alfa AF: 0.444 Hom.: 19121

Bravo AF: 0.483

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2738046; hg19: chr8-6823542;