rs916786

Variant names:

• chr7-110414465-C-T
• rs916786
• ENST00000843181.1:n.362C>T

Variant summary

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

The ENST00000843181.1(ENSG00000309703):​n.362C>T variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,972 control chromosomes in the GnomAD database, including 19,290 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 0.50 (19290 hom., cov: 33)
• Consequence: ENSG00000309703 ENST00000843181.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

Genes affected

ENSG00000309703 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843181.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309703	ENST00000843181.1		n.362C>T		splice_region non_coding_transcript_exon	Exon 1 of 2
	ENSG00000226965	ENST00000658032.1		n.331-49175G>A		intron	N/A
	ENSG00000226965	ENST00000666128.1		n.97+18346G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75919 AN: 151854 Hom.: 19255 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.500 AC: 76005 AN: 151972 Hom.: 19290 Cov.: 33 AF XY: 0.501 AC XY: 37239 AN XY: 74286

African (AFR) AF: 0.552 AC: 22907 AN: 41472

American (AMR) AF: 0.494 AC: 7546 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1681 AN: 3464

East Asian (EAS) AF: 0.626 AC: 3220 AN: 5146

South Asian (SAS) AF: 0.594 AC: 2863 AN: 4816

European-Finnish (FIN) AF: 0.399 AC: 4206 AN: 10530

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31805 AN: 67952

Other (OTH) AF: 0.512 AC: 1082 AN: 2112

Alfa AF: 0.483 Hom.: 9400

Bravo AF: 0.511

Asia WGS AF: 0.617 AC: 2135 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs916786;

hg19: chr7-110054522;