rs7785846

Variant names:

• chr7-95404529-C-T
• rs7785846
• ENST00000718462.1:n.589+7501C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000718462.1(ENSG00000233942):​n.589+7501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,080 control chromosomes in the GnomAD database, including 5,885 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 0.27 (5885 hom., cov: 32)
• Consequence: ENSG00000233942 ENST00000718462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 14 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986822	XR_007060439.1	n.557+7501C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233942	ENST00000718462.1	n.589+7501C>T		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818771.1	n.521+7501C>T		intron_variant	Intron 1 of 8
ENSG00000233942	ENST00000818772.1	n.463+7501C>T		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818773.1	n.435+7501C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40713 AN: 151962 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.268 AC: 40758 AN: 152080 Hom.: 5885 Cov.: 32 AF XY: 0.277 AC XY: 20609 AN XY: 74326

African (AFR) AF: 0.285 AC: 11837 AN: 41476

American (AMR) AF: 0.220 AC: 3362 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3470

East Asian (EAS) AF: 0.191 AC: 989 AN: 5166

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4818

European-Finnish (FIN) AF: 0.450 AC: 4755 AN: 10556

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16511 AN: 67996

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.236 Hom.: 5488

Bravo AF: 0.246

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7785846; hg19: chr7-95033841;