chr6-141214840-G-C

Variant names:

• chr6-141214840-G-C
• rs718176

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 0.311 in 151,842 control chromosomes in the GnomAD database, including 7,664 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 0.31 (7664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.311 AC: 47250 AN: 151722 Hom.: 7659 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.311 AC: 47265 AN: 151842 Hom.: 7664 Cov.: 32 AF XY: 0.308 AC XY: 22854 AN XY: 74194

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.335

Alfa AF: 0.338 Hom.: 1124

Bravo AF: 0.311

Asia WGS AF: 0.252 AC: 874 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718176; hg19: chr6-141535977;