rs7775425

Positions:

• chr6-23404048-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000658716.1(ENSG00000235743):​n.347T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,194 control chromosomes in the GnomAD database, including 1,511 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 0.13 (1511 hom., cov: 33)
• Consequence: ENST00000658716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.481+53542A>G		intron_variant, non_coding_transcript_variant
LOC124900213	XR_007059502.1	n.1017T>C		non_coding_transcript_exon_variant	6/6
LOC124900213	XR_007059503.1	n.1000T>C		non_coding_transcript_exon_variant	6/6
LOC105374976	XR_007059501.1	n.459+53542A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658716.1	n.347T>C		non_coding_transcript_exon_variant	3/3
	ENST00000690652.2	n.291+53542A>G		intron_variant, non_coding_transcript_variant
	ENST00000700866.1	n.262-31919A>G		intron_variant, non_coding_transcript_variant
	ENST00000702216.1	n.284-24680A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19731 AN: 152076 Hom.: 1505 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.130 AC: 19767 AN: 152194 Hom.: 1511 Cov.: 33 AF XY: 0.129 AC XY: 9626 AN XY: 74408

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0917

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0983 Hom.: 1124

Bravo AF: 0.135

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	13
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7775425; hg19: chr6-23404276;