chr6-118332041-G-C

Position:

• chr6-118332041-G-C

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 0.0357 in 152,308 control chromosomes in the GnomAD database, including 147 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 0.036 (147 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5446 AN: 152190 Hom.: 148 Cov.: 33

Gnomad AFR AF: 0.00955

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0357 AC: 5442 AN: 152308 Hom.: 147 Cov.: 33 AF XY: 0.0354 AC XY: 2636 AN XY: 74466

Gnomad4 AFR AF: 0.00952

Gnomad4 AMR AF: 0.0270

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0718

Gnomad4 FIN AF: 0.0356

Gnomad4 NFE AF: 0.0534

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0448 Hom.: 108

Bravo AF: 0.0326

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12210810; hg19: chr6-118653204;