rs12191601

Variant names:

• chr6-93116955-G-T
• rs12191601

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0266 in 151,844 control chromosomes in the GnomAD database, including 59 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 0.027 (59 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0266 (4034/151844) while in subpopulation NFE AF = 0.0376 (2551/67888). AF 95% confidence interval is 0.0364. There are 59 homozygotes in GnomAd4. There are 1947 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 59 gene

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: 0.0266 AC: 4034 AN: 151726 Hom.: 59 Cov.: 31

Gnomad AFR AF: 0.00719

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0242

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0154

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0376

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0266 AC: 4034 AN: 151844 Hom.: 59 Cov.: 31 AF XY: 0.0262 AC XY: 1947 AN XY: 74196

African (AFR) AF: 0.00717 AC: 297 AN: 41450

American (AMR) AF: 0.0241 AC: 366 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5136

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4814

European-Finnish (FIN) AF: 0.0504 AC: 533 AN: 10570

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0376 AC: 2551 AN: 67888

Other (OTH) AF: 0.0289 AC: 61 AN: 2108

Alfa AF: 0.0288 Hom.: 38

Bravo AF: 0.0232

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.61
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs12191601; hg19: chr6-93826673;