7-140242504-G-A

Position:

• chr7-140242504-G-A

Variant summary

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

The XR_001745386.2(LOC107986854):​n.136+10883G>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 0.391 in 152,084 control chromosomes in the GnomAD database, including 12,305 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 0.39 (12305 hom., cov: 32)
• Consequence: LOC107986854 XR_001745386.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771

Genes affected

LOC107986854 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986854	XR_001745386.2	n.136+10883G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59414 AN: 151966 Hom.: 12302 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.391 AC: 59422 AN: 152084 Hom.: 12305 Cov.: 32 AF XY: 0.388 AC XY: 28836 AN XY: 74338

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.401

Alfa AF: 0.433 Hom.: 18082

Bravo AF: 0.402

Asia WGS AF: 0.440 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11977670; hg19: chr7-139942304;