8-42207986-T-C

Variant names:

• chr8-42207986-T-C
• rs8178674

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0698 in 151,616 control chromosomes in the GnomAD database, including 1,197 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 0.070 (1197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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: 0.0696 AC: 10538 AN: 151496 Hom.: 1190 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.00550

Gnomad EAS AF: 0.00487

Gnomad SAS AF: 0.00565

Gnomad FIN AF: 0.000284

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00274

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0698 AC: 10580 AN: 151616 Hom.: 1197 Cov.: 32 AF XY: 0.0674 AC XY: 4996 AN XY: 74094

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.00550

Gnomad4 EAS AF: 0.00449

Gnomad4 SAS AF: 0.00523

Gnomad4 FIN AF: 0.000284

Gnomad4 NFE AF: 0.00274

Gnomad4 OTH AF: 0.0470

Alfa AF: 0.0384 Hom.: 86

Bravo AF: 0.0796

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8178674; hg19: chr8-42065504;