8-128192778-T-C

Variant names:

• chr8-128192778-T-C
• rs12707927

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 0.933 in 152,234 control chromosomes in the GnomAD database, including 66,829 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 0.93 (66829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.42
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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: 0.933 AC: 141924 AN: 152116 Hom.: 66761 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.933 AC: 142059 AN: 152234 Hom.: 66829 Cov.: 32 AF XY: 0.927 AC XY: 68984 AN XY: 74418

African (AFR) AF: 0.984 AC: 40909 AN: 41560

American (AMR) AF: 0.892 AC: 13630 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3265 AN: 3472

East Asian (EAS) AF: 0.553 AC: 2854 AN: 5162

South Asian (SAS) AF: 0.761 AC: 3662 AN: 4814

European-Finnish (FIN) AF: 0.946 AC: 10036 AN: 10606

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.950 AC: 64610 AN: 68026

Other (OTH) AF: 0.927 AC: 1960 AN: 2114

Alfa AF: 0.938 Hom.: 93800

Bravo AF: 0.930

Asia WGS AF: 0.667 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0010
DANN	Benign	0.33
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs12707927; hg19: chr8-129205024;