8-19967617-C-T

Variant names:

• chr8-19967617-C-T
• rs4921684

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 0.138 in 152,062 control chromosomes in the GnomAD database, including 1,565 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 0.14 (1565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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: 0.138 AC: 20914 AN: 151944 Hom.: 1563 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.138 AC: 20924 AN: 152062 Hom.: 1565 Cov.: 32 AF XY: 0.138 AC XY: 10222 AN XY: 74314

African (AFR) AF: 0.0882 AC: 3656 AN: 41470

American (AMR) AF: 0.154 AC: 2352 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3472

East Asian (EAS) AF: 0.0945 AC: 488 AN: 5164

South Asian (SAS) AF: 0.129 AC: 623 AN: 4816

European-Finnish (FIN) AF: 0.157 AC: 1658 AN: 10546

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10784 AN: 67978

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.134 Hom.: 235

Bravo AF: 0.135

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.39
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4921684; hg19: chr8-19825128;