chr6-6343774-C-A

Variant names:

• chr6-6343774-C-A
• rs9328354

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 0.334 in 152,008 control chromosomes in the GnomAD database, including 8,891 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 0.33 (8891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 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: 0.333 AC: 50652 AN: 151890 Hom.: 8874 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.334 AC: 50703 AN: 152008 Hom.: 8891 Cov.: 32 AF XY: 0.330 AC XY: 24542 AN XY: 74286

African (AFR) AF: 0.317 AC: 13150 AN: 41458

American (AMR) AF: 0.343 AC: 5243 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3466

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5192

South Asian (SAS) AF: 0.152 AC: 734 AN: 4820

European-Finnish (FIN) AF: 0.377 AC: 3972 AN: 10526

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25305 AN: 67958

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.358 Hom.: 31043

Bravo AF: 0.330

Asia WGS AF: 0.0960 AC: 336 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.40
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs9328354; hg19: chr6-6344007;