rs1543239

Positions:

• chr7-69208109-G-A

Variant summary

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

The ENST00000670444.1(ENSG00000225718):​n.531-20796C>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 0.181 in 152,192 control chromosomes in the GnomAD database, including 2,617 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 0.18 (2617 hom., cov: 33)
• Consequence: ENST00000670444.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670444.1	n.531-20796C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27526 AN: 152074 Hom.: 2613 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.181 AC: 27555 AN: 152192 Hom.: 2617 Cov.: 33 AF XY: 0.182 AC XY: 13564 AN XY: 74408

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.202

Alfa AF: 0.183 Hom.: 5506

Bravo AF: 0.185

Asia WGS AF: 0.243 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1543239; hg19: chr7-68673096;