chr6-33528937-T-G

Position:

• chr6-33528937-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001743876.1(LOC107986537):​n.17+7034A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,116 control chromosomes in the GnomAD database, including 14,749 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 0.40 (14749 hom., cov: 32)
• Consequence: LOC107986537 XR_001743876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

Genes affected

LOC107986537 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986537	XR_001743876.1	n.17+7034A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61276 AN: 151998 Hom.: 14707 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.403 AC: 61359 AN: 152116 Hom.: 14749 Cov.: 32 AF XY: 0.390 AC XY: 28972 AN XY: 74380

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.410

Alfa AF: 0.336 Hom.: 14337

Bravo AF: 0.430

Asia WGS AF: 0.186 AC: 649 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	0.58
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs449242; hg19: chr6-33496714;