7-44994240-T-C

Position:

• chr7-44994240-T-C

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 0.489 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.44994240T>C		intergenic_region
LOC102723334	XR_428139.4	n.501+789A>G		intron_variant
LOC102723334	XR_927229.3	n.666+789A>G		intron_variant
LOC102723334	XR_927230.3	n.282+789A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.528

Alfa AF: 0.508 Hom.: 2464

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4724339; hg19: chr7-45033839;