chr12-97955560-G-A

Variant names:

• chr12-97955560-G-A
• rs10492267

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 0.112 in 151,970 control chromosomes in the GnomAD database, including 1,511 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 0.11 (1511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.112 AC: 16937 AN: 151854 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.112 AC: 16966 AN: 151970 Hom.: 1511 Cov.: 32 AF XY: 0.120 AC XY: 8939 AN XY: 74252

African (AFR) AF: 0.132 AC: 5459 AN: 41454

American (AMR) AF: 0.220 AC: 3358 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0641 AC: 222 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1955 AN: 5132

South Asian (SAS) AF: 0.273 AC: 1311 AN: 4800

European-Finnish (FIN) AF: 0.0836 AC: 883 AN: 10568

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0507 AC: 3450 AN: 67988

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.0866 Hom.: 240

Bravo AF: 0.121

Asia WGS AF: 0.381 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.32
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10492267; hg19: chr12-98349338;