chr6-115851928-C-G

Variant names:

• chr6-115851928-C-G
• rs195478

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 0.343 in 149,392 control chromosomes in the GnomAD database, including 9,077 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 0.34 (9077 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.473 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: 0.343 AC: 51175 AN: 149288 Hom.: 9066 Cov.: 29

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.343 AC: 51220 AN: 149392 Hom.: 9077 Cov.: 29 AF XY: 0.343 AC XY: 24949 AN XY: 72694

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.385

Alfa AF: 0.318 Hom.: 992

Bravo AF: 0.361

Asia WGS AF: 0.343 AC: 1192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs195478; hg19: chr6-116173092;