6-89143977-A-T

Variant summary

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

The ENST00000657573.1(ENSG00000288009):n.294-144T>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 0.267 in 152,178 control chromosomes in the GnomAD database, including 5,533 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 0.27 (5533 hom., cov: 33)
• Consequence: ENST00000657573.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929004	XR_942766.4	n.1175-144T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657573.1	n.294-144T>A		intron_variant, non_coding_transcript_variant
	ENST00000664569.1	n.247-144T>A		intron_variant, non_coding_transcript_variant
	ENST00000665193.1	n.264-144T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40578 AN: 152060 Hom.: 5516 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.267 AC: 40637 AN: 152178 Hom.: 5533 Cov.: 33 AF XY: 0.261 AC XY: 19451 AN XY: 74408

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.282

Alfa AF: 0.258 Hom.: 681

Bravo AF: 0.278

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.5
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10223547; hg19: chr6-89853696;