rs808276

chr10-114805628-A-Gchr10-114805628-A-T

Variant summary

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

The XM_047426127.1(LOC124902508):c.*224-7212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,074 control chromosomes in the GnomAD database, including 27,857 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 0.60 (27857 hom., cov: 32)
• Consequence: LOC124902508 XM_047426127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

LOC124902508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902508	XM_047426127.1	c.*224-7212T>C		intron_variant
LOC124902508	XM_047426125.1	c.*224-5185T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91556 AN: 151956 Hom.: 27820 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.603 AC: 91661 AN: 152074 Hom.: 27857 Cov.: 32 AF XY: 0.597 AC XY: 44357 AN XY: 74324

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.597

Alfa AF: 0.596 Hom.: 15686

Bravo AF: 0.610

Asia WGS AF: 0.568 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.4
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs808276; hg19: chr10-116565387;