chr6-28240757-T-C

Variant names:

• chr6-28240757-T-C
• rs1150711

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 0.468 in 151,960 control chromosomes in the GnomAD database, including 20,114 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 0.47 (20114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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: 0.467 AC: 70948 AN: 151842 Hom.: 20057 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.468 AC: 71065 AN: 151960 Hom.: 20114 Cov.: 32 AF XY: 0.465 AC XY: 34516 AN XY: 74274

African (AFR) AF: 0.794 AC: 32886 AN: 41416

American (AMR) AF: 0.444 AC: 6786 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3466

East Asian (EAS) AF: 0.556 AC: 2868 AN: 5154

South Asian (SAS) AF: 0.494 AC: 2379 AN: 4818

European-Finnish (FIN) AF: 0.258 AC: 2726 AN: 10576

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20676 AN: 67950

Other (OTH) AF: 0.465 AC: 980 AN: 2108

Alfa AF: 0.369 Hom.: 37777

Bravo AF: 0.499

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.24
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1150711; hg19: chr6-28208535;