6-43828231-G-T

Position:

• chr6-43828231-G-T

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-14280G>T 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 0.835 in 152,194 control chromosomes in the GnomAD database, including 53,702 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 0.84 (53702 hom., cov: 33)
• Consequence: ENST00000637813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375070	XR_007059588.1	n.193-14280G>T		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+298960G>T		intron_variant
LOC105375070	XR_007059589.1	n.193-14280G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000637813.1	n.366-14280G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.835 AC: 127018 AN: 152076 Hom.: 53657 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.835 AC: 127120 AN: 152194 Hom.: 53702 Cov.: 33 AF XY: 0.835 AC XY: 62109 AN XY: 74416

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.826

Alfa AF: 0.897 Hom.: 91194

Bravo AF: 0.819

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs943072; hg19: chr6-43795968;