4-104923116-T-G

Variant names:

• chr4-104923116-T-G
• rs10005603
• ENST00000506148.6:n.175+15656T>G

Variant summary

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

The ENST00000506148.6(ENSG00000248373):​n.175+15656T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,036 control chromosomes in the GnomAD database, including 1,840 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 0.12 (1840 hom., cov: 32)
• Consequence: ENSG00000248373 ENST00000506148.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 6 publications found

Genes affected

ENSG00000248373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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
ENSG00000248373	ENST00000506148.6	n.175+15656T>G		intron_variant	Intron 1 of 4	5
ENSG00000248242	ENST00000515127.1	n.366+4879A>C		intron_variant	Intron 3 of 5	5
ENSG00000248373	ENST00000515649.3	n.693+15656T>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18699 AN: 151918 Hom.: 1836 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.0617

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.123 AC: 18731 AN: 152036 Hom.: 1840 Cov.: 32 AF XY: 0.121 AC XY: 8995 AN XY: 74326

African (AFR) AF: 0.274 AC: 11347 AN: 41466

American (AMR) AF: 0.0914 AC: 1392 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3470

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5188

South Asian (SAS) AF: 0.0518 AC: 250 AN: 4824

European-Finnish (FIN) AF: 0.0617 AC: 654 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4182 AN: 67942

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.0789 Hom.: 735

Bravo AF: 0.133

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.50
PhyloP100		-1.8
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: rs10005603; hg19: chr4-105844273;