rs10937624

chr4-4032235-G-T

Variant summary

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

The XR_001741557.2(LOC101928217):n.58+474G>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 0.578 in 151,842 control chromosomes in the GnomAD database, including 25,797 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 0.58 (25797 hom., cov: 32)
• Consequence: LOC101928217 XR_001741557.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

LOC101928217 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928217	XR_001741557.2	n.58+474G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87728 AN: 151722 Hom.: 25779 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.578 AC: 87789 AN: 151842 Hom.: 25797 Cov.: 32 AF XY: 0.582 AC XY: 43192 AN XY: 74218

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.592

Alfa AF: 0.563 Hom.: 3060

Bravo AF: 0.580

Asia WGS AF: 0.708 AC: 2459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.28
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10937624; hg19: chr4-4033962;