rs10516441

Positions:

• chr4-99386010-G-A
• chr4-99386010-G-C

Variant summary

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

The XR_939020.3(LOC102723576):​n.1285-2390C>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 0.0788 in 152,110 control chromosomes in the GnomAD database, including 1,676 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 0.079 (1676 hom., cov: 32)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.1285-2390C>T		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.388-2390C>T		intron_variant, non_coding_transcript_variant
LOC102723576	XR_427569.4	n.1285-2390C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11990 AN: 151992 Hom.: 1678 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.0955

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0788 AC: 11987 AN: 152110 Hom.: 1676 Cov.: 32 AF XY: 0.0883 AC XY: 6562 AN XY: 74346

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.0955

Gnomad4 NFE AF: 0.0649

Gnomad4 OTH AF: 0.0579

Alfa AF: 0.0777 Hom.: 413

Bravo AF: 0.0699

Asia WGS AF: 0.389 AC: 1350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516441; hg19: chr4-100307167;