chr6-23437448-C-A

Position:

• chr6-23437448-C-A

Variant summary

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

The ENST00000690652.2(ENSG00000289368):​n.291+20142G>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 0.0337 in 152,074 control chromosomes in the GnomAD database, including 146 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 0.034 (146 hom., cov: 32)
• Consequence: ENST00000690652.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.481+20142G>T		intron_variant, non_coding_transcript_variant
LOC105374975	XR_001744048.2	n.89-4132C>A		intron_variant, non_coding_transcript_variant
LOC105374976	XR_007059501.1	n.459+20142G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000690652.2	n.291+20142G>T		intron_variant, non_coding_transcript_variant
	ENST00000700866.1	n.261+20142G>T		intron_variant, non_coding_transcript_variant
	ENST00000702216.1	n.283+20142G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0336 AC: 5101 AN: 151956 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0337 AC: 5119 AN: 152074 Hom.: 146 Cov.: 32 AF XY: 0.0366 AC XY: 2719 AN XY: 74362

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.0763

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.0550

Gnomad4 SAS AF: 0.0689

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0189 Hom.: 57

Bravo AF: 0.0378

Asia WGS AF: 0.0860 AC: 298 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7771911; hg19: chr6-23437676;