chr7-110414465-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.386+18346G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309703	ENST00000843181.1	n.362C>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000226965	ENST00000658032.1	n.331-49175G>A		intron_variant	Intron 3 of 5
ENSG00000226965	ENST00000666128.1	n.97+18346G>A		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs916786; hg19: chr7-110054522;