6-1402302-T-C

Variant names:

• chr6-1402302-T-C
• rs1711973

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 0.784 in 152,082 control chromosomes in the GnomAD database, including 47,287 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 0.78 (47287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.784 AC: 119180 AN: 151964 Hom.: 47239 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.784 AC: 119291 AN: 152082 Hom.: 47287 Cov.: 32 AF XY: 0.787 AC XY: 58506 AN XY: 74330

African (AFR) AF: 0.856 AC: 35483 AN: 41474

American (AMR) AF: 0.813 AC: 12433 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2963 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5166 AN: 5172

South Asian (SAS) AF: 0.901 AC: 4343 AN: 4818

European-Finnish (FIN) AF: 0.666 AC: 7042 AN: 10580

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49111 AN: 67964

Other (OTH) AF: 0.807 AC: 1705 AN: 2114

Alfa AF: 0.752 Hom.: 74490

Bravo AF: 0.800

Asia WGS AF: 0.944 AC: 3282 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	4.4
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1711973; hg19: chr6-1402537;