rs6454338

chr6-83783631-G-Cchr6-83783631-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 0.582 in 152,060 control chromosomes in the GnomAD database, including 30,839 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 0.58 (30839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

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 (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88415 AN: 151942 Hom.: 30841 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.582 AC: 88427 AN: 152060 Hom.: 30839 Cov.: 32 AF XY: 0.585 AC XY: 43509 AN XY: 74334

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.587

Alfa AF: 0.675 Hom.: 4764

Bravo AF: 0.540

Asia WGS AF: 0.564 AC: 1963 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	3.4
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: rs6454338; hg19: chr6-84493350; COSMIC: COSV64076862;