4-104923116-T-G

Position:

• chr4-104923116-T-G

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.104923116T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248373	ENST00000506148.5	n.104+15656T>G		intron_variant		5
ENSG00000248242	ENST00000515127.1	n.366+4879A>C		intron_variant		5
ENSG00000248373	ENST00000515649.2	n.693+15656T>G		intron_variant		3
ENSG00000248373	ENST00000671069.1	n.197-495T>G		intron_variant

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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.0518

Gnomad4 FIN AF: 0.0617

Gnomad4 NFE AF: 0.0616

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0656 Hom.: 288

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10005603; hg19: chr4-105844273;