6-148170438-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 0.622 in 151,856 control chromosomes in the GnomAD database, including 29,810 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 0.62 (29810 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

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 = 0.711 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: 0.622 AC: 94332 AN: 151738 Hom.: 29790 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.622 AC: 94393 AN: 151856 Hom.: 29810 Cov.: 31 AF XY: 0.619 AC XY: 45955 AN XY: 74228

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.623

Alfa AF: 0.586 Hom.: 52153

Bravo AF: 0.630

Asia WGS AF: 0.543 AC: 1890 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	2.1
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6570819; hg19: chr6-148491574;