chr8-42207986-T-C

Position:

• chr8-42207986-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;