8-131665346-C-T

Variant names:

• chr8-131665346-C-T
• rs4406373

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 0.209 in 152,142 control chromosomes in the GnomAD database, including 3,547 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 0.21 (3547 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.414 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: 0.209 AC: 31743 AN: 152024 Hom.: 3540 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.209 AC: 31750 AN: 152142 Hom.: 3547 Cov.: 33 AF XY: 0.211 AC XY: 15673 AN XY: 74376

African (AFR) AF: 0.185 AC: 7673 AN: 41520

American (AMR) AF: 0.156 AC: 2378 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5164

South Asian (SAS) AF: 0.429 AC: 2069 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2053 AN: 10578

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14514 AN: 67984

Other (OTH) AF: 0.224 AC: 473 AN: 2116

Alfa AF: 0.202 Hom.: 1932

Bravo AF: 0.199

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4406373; hg19: chr8-132677593;