7-44994240-T-C

Variant names:

• chr7-44994240-T-C
• rs4724339
• ENST00000842803.1:n.412+789A>G

Variant summary

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

The ENST00000842803.1(ENSG00000309655):​n.412+789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 150,378 control chromosomes in the GnomAD database, including 19,383 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 0.49 (19383 hom., cov: 29)
• Consequence: ENSG00000309655 ENST00000842803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 1 publications found

Genes affected

ENSG00000309655 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723334	XR_428139.4	n.501+789A>G		intron_variant	Intron 3 of 3
LOC102723334	XR_927229.3	n.666+789A>G		intron_variant	Intron 4 of 4
LOC102723334	XR_927230.3	n.282+789A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309655	ENST00000842803.1	n.412+789A>G		intron_variant	Intron 2 of 3
ENSG00000309655	ENST00000842804.1	n.505+789A>G		intron_variant	Intron 3 of 4
ENSG00000309655	ENST00000842805.1	n.392+789A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 73450 AN: 150266 Hom.: 19381 Cov.: 29

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.489 AC: 73464 AN: 150378 Hom.: 19383 Cov.: 29 AF XY: 0.493 AC XY: 36051 AN XY: 73138

African (AFR) AF: 0.280 AC: 11460 AN: 40932

American (AMR) AF: 0.500 AC: 7536 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1845 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3760 AN: 5102

South Asian (SAS) AF: 0.436 AC: 2086 AN: 4782

European-Finnish (FIN) AF: 0.652 AC: 6431 AN: 9864

Middle Eastern (MID) AF: 0.541 AC: 157 AN: 290

European-Non Finnish (NFE) AF: 0.567 AC: 38494 AN: 67858

Other (OTH) AF: 0.528 AC: 1102 AN: 2086

Alfa AF: 0.498 Hom.: 2498

Bravo AF: 0.476

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.78
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4724339; hg19: chr7-45033839;