6-89324017-C-T

Variant names:

• chr6-89324017-C-T
• rs12195070

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 0.17 in 152,214 control chromosomes in the GnomAD database, including 2,295 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 0.17 (2295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 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: 0.170 AC: 25917 AN: 152096 Hom.: 2293 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.170 AC: 25941 AN: 152214 Hom.: 2295 Cov.: 32 AF XY: 0.173 AC XY: 12856 AN XY: 74434

African (AFR) AF: 0.134 AC: 5572 AN: 41522

American (AMR) AF: 0.192 AC: 2944 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 862 AN: 3466

East Asian (EAS) AF: 0.190 AC: 986 AN: 5184

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4824

European-Finnish (FIN) AF: 0.145 AC: 1537 AN: 10606

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11952 AN: 67998

Other (OTH) AF: 0.206 AC: 436 AN: 2112

Alfa AF: 0.183 Hom.: 4455

Bravo AF: 0.170

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.51
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs12195070; hg19: chr6-90033736;