6-71484004-A-C

Variant names:

• chr6-71484004-A-C
• rs9351814

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 0.361 in 151,918 control chromosomes in the GnomAD database, including 10,438 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 0.36 (10438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.361 AC: 54811 AN: 151800 Hom.: 10441 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.361 AC: 54836 AN: 151918 Hom.: 10438 Cov.: 32 AF XY: 0.370 AC XY: 27445 AN XY: 74230

African (AFR) AF: 0.260 AC: 10794 AN: 41452

American (AMR) AF: 0.444 AC: 6767 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3464

East Asian (EAS) AF: 0.550 AC: 2833 AN: 5154

South Asian (SAS) AF: 0.507 AC: 2438 AN: 4810

European-Finnish (FIN) AF: 0.406 AC: 4274 AN: 10528

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.371 AC: 25232 AN: 67950

Other (OTH) AF: 0.363 AC: 765 AN: 2108

Alfa AF: 0.373 Hom.: 43743

Bravo AF: 0.362

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.32
DANN	Benign	0.51
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs9351814; hg19: chr6-72193707;