rs7576174

chr2-42091824-C-T

Variant summary

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

The XR_940001.1(LOC105374531):n.177+5793G>A 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 0.145 in 152,126 control chromosomes in the GnomAD database, including 2,734 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 0.14 (2734 hom., cov: 32)
• Consequence: LOC105374531 XR_940001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

LOC105374531 (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 = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374531	XR_940001.1	n.177+5793G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21962 AN: 152006 Hom.: 2724 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.145 AC: 22001 AN: 152126 Hom.: 2734 Cov.: 32 AF XY: 0.143 AC XY: 10642 AN XY: 74396

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0754

Gnomad4 NFE AF: 0.0581

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0817 Hom.: 707

Bravo AF: 0.152

Asia WGS AF: 0.130 AC: 451 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	0.66
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7576174; hg19: chr2-42318964;