rs7975663

Variant names:

• chr12-107145187-A-C
• rs7975663

Your query was ambiguous. Multiple possible variants found:

• chr12-107145187-A-C
• chr12-107145187-A-T

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 0.181 in 152,078 control chromosomes in the GnomAD database, including 3,095 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 0.18 (3095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.181 AC: 27567 AN: 151960 Hom.: 3099 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.181 AC: 27582 AN: 152078 Hom.: 3095 Cov.: 32 AF XY: 0.185 AC XY: 13785 AN XY: 74350

African (AFR) AF: 0.207 AC: 8606 AN: 41476

American (AMR) AF: 0.218 AC: 3326 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 529 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2993 AN: 5160

South Asian (SAS) AF: 0.199 AC: 956 AN: 4808

European-Finnish (FIN) AF: 0.126 AC: 1331 AN: 10602

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9247 AN: 67968

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.156 Hom.: 4533

Bravo AF: 0.194

Asia WGS AF: 0.374 AC: 1298 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	2.6
DANN	Benign	0.63
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7975663; hg19: chr12-107538965;