chr5-92654409-C-T

Variant names:

• chr5-92654409-C-T
• rs7710144
• ENST00000513779.1:n.134+6321G>A

Variant summary

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

The ENST00000513779.1(ENSG00000249776):​n.134+6321G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,324 control chromosomes in the GnomAD database, including 1,428 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 0.11 (1428 hom., cov: 32)
• Consequence: ENSG00000249776 ENST00000513779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

ENSG00000249776 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379082	NR_188296.1	n.362+15343G>A		intron_variant	Intron 3 of 3
LOC105379082	NR_188297.1	n.217+17075G>A		intron_variant	Intron 2 of 2
LOC105379082	NR_188298.1	n.217+17075G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249776	ENST00000513779.1	n.134+6321G>A		intron_variant	Intron 1 of 2	3
ENSG00000249776	ENST00000718057.1	n.390+15343G>A		intron_variant	Intron 3 of 5
ENSG00000249776	ENST00000850101.1	n.256+17075G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17102 AN: 151208 Hom.: 1414 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.0746

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.113 AC: 17139 AN: 151324 Hom.: 1428 Cov.: 32 AF XY: 0.110 AC XY: 8128 AN XY: 73906

African (AFR) AF: 0.231 AC: 9544 AN: 41260

American (AMR) AF: 0.0713 AC: 1080 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 460 AN: 3472

East Asian (EAS) AF: 0.0296 AC: 152 AN: 5130

South Asian (SAS) AF: 0.0747 AC: 358 AN: 4794

European-Finnish (FIN) AF: 0.0336 AC: 350 AN: 10406

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0725 AC: 4917 AN: 67816

Other (OTH) AF: 0.0914 AC: 192 AN: 2100

Alfa AF: 0.0742 Hom.: 338

Bravo AF: 0.120

Asia WGS AF: 0.0570 AC: 200 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.15
PhyloP100		-0.043
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7710144; hg19: chr5-91990116;