6-153561202-T-G

Variant names:

• chr6-153561202-T-G
• rs9384111

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 0.157 in 151,776 control chromosomes in the GnomAD database, including 2,597 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 0.16 (2597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 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: 0.157 AC: 23821 AN: 151672 Hom.: 2588 Cov.: 32

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.157 AC: 23846 AN: 151776 Hom.: 2597 Cov.: 32 AF XY: 0.164 AC XY: 12188 AN XY: 74184

African (AFR) AF: 0.0441 AC: 1831 AN: 41482

American (AMR) AF: 0.322 AC: 4888 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3466

East Asian (EAS) AF: 0.296 AC: 1531 AN: 5172

South Asian (SAS) AF: 0.373 AC: 1798 AN: 4816

European-Finnish (FIN) AF: 0.158 AC: 1651 AN: 10442

Middle Eastern (MID) AF: 0.101 AC: 29 AN: 288

European-Non Finnish (NFE) AF: 0.167 AC: 11308 AN: 67892

Other (OTH) AF: 0.167 AC: 351 AN: 2104

Alfa AF: 0.160 Hom.: 3697

Bravo AF: 0.161

Asia WGS AF: 0.319 AC: 1105 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.44
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs9384111; hg19: chr6-153882337; COSMIC: COSV60293340;