6-132818471-C-G

Variant names:

• chr6-132818471-C-G
• rs9321374

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 0.434 in 152,062 control chromosomes in the GnomAD database, including 14,867 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 0.43 (14867 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.531 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: 0.434 AC: 65909 AN: 151944 Hom.: 14839 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.434 AC: 65997 AN: 152062 Hom.: 14867 Cov.: 33 AF XY: 0.434 AC XY: 32291 AN XY: 74318

African (AFR) AF: 0.537 AC: 22271 AN: 41484

American (AMR) AF: 0.541 AC: 8259 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1394 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1544 AN: 5166

South Asian (SAS) AF: 0.436 AC: 2099 AN: 4810

European-Finnish (FIN) AF: 0.365 AC: 3849 AN: 10558

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25142 AN: 67982

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.215 Hom.: 405

Bravo AF: 0.452

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.29
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9321374; hg19: chr6-133139610; COSMIC: COSV57767825;