chr6-140876209-A-T

Position:

• chr6-140876209-A-T

Variant summary

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

The ENST00000650553.2(ENSG00000234147):​n.194+21979T>A 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 0.388 in 151,910 control chromosomes in the GnomAD database, including 12,101 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 0.39 (12101 hom., cov: 32)
• Consequence: ENST00000650553.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901413	XR_007059792.1	n.322-3348A>T		intron_variant, non_coding_transcript_variant
LOC102723724	XR_428030.5	n.237+21979T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650553.2	n.194+21979T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58895 AN: 151790 Hom.: 12075 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.388 AC: 58975 AN: 151910 Hom.: 12101 Cov.: 32 AF XY: 0.384 AC XY: 28526 AN XY: 74234

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.397

Alfa AF: 0.363 Hom.: 1322

Bravo AF: 0.394

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6570426; hg19: chr6-141197346;