rs10516800

Positions:

• chr4-87970438-G-C

Variant summary

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

The XR_007058172.1(LOC124900730):​n.131+3201C>G 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 0.269 in 152,082 control chromosomes in the GnomAD database, including 5,609 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 0.27 (5609 hom., cov: 32)
• Consequence: LOC124900730 XR_007058172.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

Genes affected

LOC124900730 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900730	XR_007058172.1	n.131+3201C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40941 AN: 151964 Hom.: 5606 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.269 AC: 40979 AN: 152082 Hom.: 5609 Cov.: 32 AF XY: 0.275 AC XY: 20467 AN XY: 74342

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.278

Alfa AF: 0.264 Hom.: 699

Bravo AF: 0.262

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516800; hg19: chr4-88891590;