6-153992036-T-C

Variant names:

• chr6-153992036-T-C
• rs9384169

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 0.368 in 151,984 control chromosomes in the GnomAD database, including 10,502 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 0.37 (10502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 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: 0.368 AC: 55851 AN: 151864 Hom.: 10484 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.368 AC: 55895 AN: 151984 Hom.: 10502 Cov.: 32 AF XY: 0.377 AC XY: 28011 AN XY: 74272

African (AFR) AF: 0.330 AC: 13670 AN: 41460

American (AMR) AF: 0.507 AC: 7747 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1329 AN: 3464

East Asian (EAS) AF: 0.424 AC: 2184 AN: 5150

South Asian (SAS) AF: 0.435 AC: 2091 AN: 4808

European-Finnish (FIN) AF: 0.445 AC: 4692 AN: 10542

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22924 AN: 67966

Other (OTH) AF: 0.370 AC: 780 AN: 2108

Alfa AF: 0.366 Hom.: 3487

Bravo AF: 0.367

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.81
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9384169; hg19: chr6-154313171; COSMIC: COSV107167860;