rs7775425

Variant names:

• chr6-23404048-T-C
• rs7775425
• ENST00000658716.1:n.347T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_187789.1(LOC102724749):​n.1375T>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: LOC102724749 NR_187789.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 2 publications found

Genes affected

ENSG00000235743 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187789.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102724749	NR_187789.1		n.1375T>C		non_coding_transcript_exon	Exon 8 of 8
	LOC102724749	NR_187790.1		n.1153T>C		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235743	ENST00000658716.1		n.347T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000235743	ENST00000814939.1		n.371T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000235743	ENST00000814943.1		n.296T>C		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.222 AC: 9216 AN: 41508

American (AMR) AF: 0.0914 AC: 1398 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3472

East Asian (EAS) AF: 0.153 AC: 791 AN: 5168

South Asian (SAS) AF: 0.0752 AC: 363 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1128 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0917 AC: 6239 AN: 68008

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.101 Hom.: 1572

Bravo AF: 0.135

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	13
DANN	Benign	0.67
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7775425; hg19: chr6-23404276;