6-152644949-T-C

Variant names:

• chr6-152644949-T-C
• rs2758813

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 0.77 in 152,174 control chromosomes in the GnomAD database, including 45,641 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 0.77 (45641 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.770 AC: 117078 AN: 152054 Hom.: 45612 Cov.: 33

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.770 AC: 117154 AN: 152174 Hom.: 45641 Cov.: 33 AF XY: 0.763 AC XY: 56761 AN XY: 74376

African (AFR) AF: 0.897 AC: 37249 AN: 41544

American (AMR) AF: 0.724 AC: 11066 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2404 AN: 3472

East Asian (EAS) AF: 0.817 AC: 4227 AN: 5172

South Asian (SAS) AF: 0.644 AC: 3106 AN: 4820

European-Finnish (FIN) AF: 0.661 AC: 6986 AN: 10564

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49695 AN: 67994

Other (OTH) AF: 0.771 AC: 1630 AN: 2114

Alfa AF: 0.755 Hom.: 8465

Bravo AF: 0.784

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.22
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2758813; hg19: chr6-152966084;