chr6-131805180-A-G

Position:

• chr6-131805180-A-G

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 0.215 in 152,052 control chromosomes in the GnomAD database, including 5,280 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 0.22 (5280 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.131805180A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32655 AN: 151934 Hom.: 5264 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.215 AC: 32716 AN: 152052 Hom.: 5280 Cov.: 32 AF XY: 0.219 AC XY: 16245 AN XY: 74314

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0952

Gnomad4 OTH AF: 0.203

Alfa AF: 0.124 Hom.: 2106

Bravo AF: 0.231

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6935458; hg19: chr6-132126320; COSMIC: COSV62935714;