8-42742089-C-G

Variant names:

• chr8-42742089-C-G
• rs6987323

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 0.034 in 152,274 control chromosomes in the GnomAD database, including 133 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 0.034 (133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0935 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: 0.0341 AC: 5193 AN: 152156 Hom.: 133 Cov.: 32

Gnomad AFR AF: 0.00951

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0340 AC: 5183 AN: 152274 Hom.: 133 Cov.: 32 AF XY: 0.0347 AC XY: 2581 AN XY: 74448

African (AFR) AF: 0.00948 AC: 394 AN: 41552

American (AMR) AF: 0.0297 AC: 454 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.101 AC: 486 AN: 4816

European-Finnish (FIN) AF: 0.0496 AC: 526 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2793 AN: 68030

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.00902 Hom.: 1

Bravo AF: 0.0309

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.94
DANN	Benign	0.29
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6987323; hg19: chr8-42597232;