rs2023890

Positions:

• chr7-24293128-G-A
• chr7-24293128-G-C

Variant summary

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

The XR_001745132.2(LOC107986777):​n.209+26229C>T 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 0.767 in 152,156 control chromosomes in the GnomAD database, including 45,017 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 0.77 (45017 hom., cov: 31)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+26229C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116586 AN: 152038 Hom.: 44992 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.767 AC: 116659 AN: 152156 Hom.: 45017 Cov.: 31 AF XY: 0.771 AC XY: 57331 AN XY: 74392

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.786

Alfa AF: 0.770 Hom.: 5642

Bravo AF: 0.767

Asia WGS AF: 0.857 AC: 2980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2023890; hg19: chr7-24332747;