6-152891987-T-C

Variant names:

• chr6-152891987-T-C
• rs13196491

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 0.0474 in 152,262 control chromosomes in the GnomAD database, including 334 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 0.047 (334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 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: 0.0474 AC: 7219 AN: 152144 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0474 AC: 7217 AN: 152262 Hom.: 334 Cov.: 32 AF XY: 0.0511 AC XY: 3803 AN XY: 74460

African (AFR) AF: 0.0129 AC: 536 AN: 41566

American (AMR) AF: 0.0261 AC: 399 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.131 AC: 674 AN: 5162

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4824

European-Finnish (FIN) AF: 0.0618 AC: 656 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3592 AN: 68010

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0497 Hom.: 182

Bravo AF: 0.0383

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs13196491; hg19: chr6-153213122;