4-104397760-G-T

Variant names:

• chr4-104397760-G-T
• rs951085
• ENST00000514327.5:n.416+1546G>T

Variant summary

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

The ENST00000514327.5(ENSG00000251170):​n.416+1546G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,800 control chromosomes in the GnomAD database, including 29,073 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 0.60 (29073 hom., cov: 31)
• Consequence: ENSG00000251170 ENST00000514327.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 2 publications found

Genes affected

ENSG00000251170 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251170	ENST00000514327.5	n.416+1546G>T		intron_variant	Intron 5 of 5	4

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91231 AN: 151682 Hom.: 29077 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.601 AC: 91257 AN: 151800 Hom.: 29073 Cov.: 31 AF XY: 0.596 AC XY: 44216 AN XY: 74208

African (AFR) AF: 0.448 AC: 18545 AN: 41362

American (AMR) AF: 0.579 AC: 8824 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2633 AN: 3468

East Asian (EAS) AF: 0.164 AC: 846 AN: 5148

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4818

European-Finnish (FIN) AF: 0.690 AC: 7268 AN: 10538

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48005 AN: 67920

Other (OTH) AF: 0.629 AC: 1324 AN: 2106

Alfa AF: 0.676 Hom.: 13211

Bravo AF: 0.586

Asia WGS AF: 0.386 AC: 1332 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.24
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs951085; hg19: chr4-105318917;