6-18349135-C-T

Variant names:

• chr6-18349135-C-T
• rs1408445

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.887 in 152,296 control chromosomes in the GnomAD database, including 60,051 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 0.89 (60051 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.887 AC: 135029 AN: 152178 Hom.: 60003 Cov.: 34

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.887 AC: 135133 AN: 152296 Hom.: 60051 Cov.: 34 AF XY: 0.891 AC XY: 66371 AN XY: 74478

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.882

Alfa AF: 0.884 Hom.: 77997

Bravo AF: 0.885

Asia WGS AF: 0.964 AC: 3351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408445; hg19: chr6-18349366;