7-34295479-C-T

Variant summary

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

The ENST00000660587.1(ENSG00000236212):n.167-2100C>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 0.374 in 151,776 control chromosomes in the GnomAD database, including 10,708 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 0.37 (10708 hom., cov: 32)
• Consequence: ENST00000660587.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 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
	ENST00000660587.1	n.167-2100C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56666 AN: 151658 Hom.: 10686 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.374 AC: 56731 AN: 151776 Hom.: 10708 Cov.: 32 AF XY: 0.374 AC XY: 27690 AN XY: 74134

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.389

Alfa AF: 0.369 Hom.: 5698

Bravo AF: 0.384

Asia WGS AF: 0.364 AC: 1267 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.31
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058163; hg19: chr7-34335091;