chr12-91074619-T-C

Variant names:

• chr12-91074619-T-C
• rs10492232

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 0.132 in 152,144 control chromosomes in the GnomAD database, including 1,497 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 0.13 (1497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.131 AC: 19985 AN: 152026 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.0663

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.132 AC: 20017 AN: 152144 Hom.: 1497 Cov.: 32 AF XY: 0.129 AC XY: 9620 AN XY: 74402

African (AFR) AF: 0.206 AC: 8550 AN: 41474

American (AMR) AF: 0.0874 AC: 1337 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3470

East Asian (EAS) AF: 0.0707 AC: 365 AN: 5166

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4824

European-Finnish (FIN) AF: 0.100 AC: 1062 AN: 10600

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7432 AN: 68000

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.117 Hom.: 465

Bravo AF: 0.135

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.52
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10492232; hg19: chr12-91468396;