chr6-139508529-C-T

Position:

• chr6-139508529-C-T

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+21914C>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 0.534 in 151,802 control chromosomes in the GnomAD database, including 22,164 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 0.53 (22164 hom., cov: 32)
• Consequence: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647815.1	n.134+21914C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81039 AN: 151684 Hom.: 22142 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.534 AC: 81091 AN: 151802 Hom.: 22164 Cov.: 32 AF XY: 0.533 AC XY: 39542 AN XY: 74162

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.556

Alfa AF: 0.563 Hom.: 13816

Bravo AF: 0.529

Asia WGS AF: 0.514 AC: 1787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.47
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs605066; hg19: chr6-139829666;