6-32038115-G-C

Position:

• chr6-32038115-G-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BS1_Supporting BS2

The variant allele was found at a frequency of 0.00381 in 585,066 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0083 (15 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (10 hom.)
• Consequence: intergenic_region
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -2.72

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00831 (1263/152060) while in subpopulation AFR AF= 0.0258 (1071/41452). AF 95% confidence interval is 0.0246. There are 15 homozygotes in gnomad4. There are 620 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32038115G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00827 AC: 1257 AN: 151942 Hom.: 15 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00563

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00103

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000648

Gnomad OTH AF: 0.00911

GnomAD4 exome AF: 0.00224 AC: 969 AN: 433006 Hom.: 10 AF XY: 0.00209 AC XY: 471 AN XY: 225384

Gnomad4 AFR exome AF: 0.0244

Gnomad4 AMR exome AF: 0.00501

Gnomad4 ASJ exome AF: 0.00773

Gnomad4 EAS exome AF: 0.00420

Gnomad4 SAS exome AF: 0.00160

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000619

Gnomad4 OTH exome AF: 0.00488

GnomAD4 genome AF: 0.00831 AC: 1263 AN: 152060 Hom.: 15 Cov.: 32 AF XY: 0.00834 AC XY: 620 AN XY: 74376

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.00563

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000648

Gnomad4 OTH AF: 0.00901

Alfa AF: 0.000364 Hom.: 0

Bravo AF: 0.0103

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.020
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130676; hg19: chr6-32005892;