7-24294032-A-T

Position:

• chr7-24294032-A-T

Variant summary

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

The XR_001745132.2(LOC107986777):​n.209+25325T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,004 control chromosomes in the GnomAD database, including 19,513 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 0.50 (19513 hom., cov: 32)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+25325T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76168 AN: 151886 Hom.: 19503 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.501 AC: 76213 AN: 152004 Hom.: 19513 Cov.: 32 AF XY: 0.506 AC XY: 37571 AN XY: 74288

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.505

Alfa AF: 0.511 Hom.: 2559

Bravo AF: 0.506

Asia WGS AF: 0.544 AC: 1888 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16473; hg19: chr7-24333651;