6-43768759-T-C

Variant names:

• chr6-43768759-T-C
• rs1005230

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 0.598 in 151,804 control chromosomes in the GnomAD database, including 28,233 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 0.60 (28233 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 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: 0.597 AC: 90620 AN: 151686 Hom.: 28203 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.598 AC: 90708 AN: 151804 Hom.: 28233 Cov.: 31 AF XY: 0.595 AC XY: 44145 AN XY: 74180

African (AFR) AF: 0.789 AC: 32649 AN: 41386

American (AMR) AF: 0.613 AC: 9361 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3735 AN: 5152

South Asian (SAS) AF: 0.552 AC: 2664 AN: 4822

European-Finnish (FIN) AF: 0.446 AC: 4677 AN: 10484

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34046 AN: 67914

Other (OTH) AF: 0.615 AC: 1294 AN: 2104

Alfa AF: 0.564 Hom.: 27004

Bravo AF: 0.623

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs1005230; hg19: chr6-43736496;