rs7174649

chr15-93289986-G-A

Variant summary

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

The ENST00000667030.1(ENSG00000257060):n.236+30749G>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 0.121 in 152,208 control chromosomes in the GnomAD database, including 1,226 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 0.12 (1226 hom., cov: 33)
• Consequence: ENST00000667030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370982	XR_007064770.1	n.1160+30749G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667030.1	n.236+30749G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18431 AN: 152090 Hom.: 1228 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.121 AC: 18423 AN: 152208 Hom.: 1226 Cov.: 33 AF XY: 0.119 AC XY: 8831 AN XY: 74410

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0744

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.134

Alfa AF: 0.122 Hom.: 294

Bravo AF: 0.125

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7174649; hg19: chr15-93833215;