rs916786

Positions:

• chr7-110414465-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667232.1(ENSG00000226965):​n.411+18346G>A variant causes a intron, non coding transcript 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: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.386+18346G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667232.1	n.411+18346G>A		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.331-49175G>A		intron_variant, non_coding_transcript_variant
	ENST00000666128.1	n.97+18346G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.512

Alfa AF: 0.483 Hom.: 8490

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916786; hg19: chr7-110054522;