chr12-104354842-A-G

Variant names:

• chr12-104354842-A-G
• rs7978310

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 0.911 in 152,258 control chromosomes in the GnomAD database, including 63,335 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 0.91 (63335 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.911 AC: 138542 AN: 152140 Hom.: 63290 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.911 AC: 138643 AN: 152258 Hom.: 63335 Cov.: 33 AF XY: 0.911 AC XY: 67831 AN XY: 74448

African (AFR) AF: 0.830 AC: 34443 AN: 41522

American (AMR) AF: 0.950 AC: 14537 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3071 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5180

South Asian (SAS) AF: 0.951 AC: 4589 AN: 4824

European-Finnish (FIN) AF: 0.922 AC: 9788 AN: 10616

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64038 AN: 68032

Other (OTH) AF: 0.923 AC: 1952 AN: 2114

Alfa AF: 0.924 Hom.: 112232

Bravo AF: 0.909

Asia WGS AF: 0.971 AC: 3375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7978310; hg19: chr12-104748620;