6-148170438-C-T

Variant names:

• chr6-148170438-C-T
• rs6570819

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.717 AC: 29722 AN: 41428

American (AMR) AF: 0.591 AC: 9012 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3189 AN: 5144

South Asian (SAS) AF: 0.510 AC: 2450 AN: 4806

European-Finnish (FIN) AF: 0.583 AC: 6139 AN: 10538

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39743 AN: 67896

Other (OTH) AF: 0.623 AC: 1315 AN: 2112

Alfa AF: 0.593 Hom.: 112500

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6570819; hg19: chr6-148491574;