rs198712

Positions:

• chr7-24141436-G-A
• chr7-24141436-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.674C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,904 control chromosomes in the GnomAD database, including 10,844 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 0.38 (10844 hom., cov: 31)
• Consequence: LOC107986777 XR_001745132.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.674C>T		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57084 AN: 151786 Hom.: 10837 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.376 AC: 57128 AN: 151904 Hom.: 10844 Cov.: 31 AF XY: 0.368 AC XY: 27334 AN XY: 74222

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.373

Alfa AF: 0.376 Hom.: 2660

Bravo AF: 0.385

Asia WGS AF: 0.311 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
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: rs198712; hg19: chr7-24181055;