7-24299750-G-T

Position:

• chr7-24299750-G-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+19607C>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 0.202 in 152,064 control chromosomes in the GnomAD database, including 3,161 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 0.20 (3161 hom., cov: 32)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+19607C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30642 AN: 151946 Hom.: 3156 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.202 AC: 30668 AN: 152064 Hom.: 3161 Cov.: 32 AF XY: 0.201 AC XY: 14930 AN XY: 74342

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.225

Alfa AF: 0.178 Hom.: 1051

Bravo AF: 0.198

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16109; hg19: chr7-24339369;