6-33968126-T-C

Variant names:

• chr6-33968126-T-C
• rs9469655

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0138 in 152,230 control chromosomes in the GnomAD database, including 35 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 0.014 (35 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0138 (2102/152230) while in subpopulation AFR AF= 0.0379 (1574/41528). AF 95% confidence interval is 0.0363. There are 35 homozygotes in gnomad4. There are 988 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 35 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: 0.0137 AC: 2088 AN: 152112 Hom.: 34 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00766

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00388

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0138 AC: 2102 AN: 152230 Hom.: 35 Cov.: 32 AF XY: 0.0133 AC XY: 988 AN XY: 74434

Gnomad4 AFR AF: 0.0379

Gnomad4 AMR AF: 0.00765

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.00312

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00388

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.00460 Hom.: 4

Bravo AF: 0.0158

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9469655; hg19: chr6-33935903;