rs62295889

chr4-12498597-T-C

Variant summary

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

The XR_001741374.1(LOC105374492):n.255-27867A>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 0.0657 in 152,000 control chromosomes in the GnomAD database, including 373 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 0.066 (373 hom., cov: 32)
• Consequence: LOC105374492 XR_001741374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

LOC105374492 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374492	XR_001741374.1	n.255-27867A>G		intron_variant, non_coding_transcript_variant
LOC105374492	XR_001741375.1	n.676-27867A>G		intron_variant, non_coding_transcript_variant
LOC105374492	XR_925406.4	n.478-27867A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9965 AN: 151882 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0876

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0657 AC: 9987 AN: 152000 Hom.: 373 Cov.: 32 AF XY: 0.0664 AC XY: 4935 AN XY: 74286

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.0432

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.0450

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.0788

Gnomad4 NFE AF: 0.0863

Gnomad4 OTH AF: 0.0536

Alfa AF: 0.0791 Hom.: 88

Bravo AF: 0.0574

Asia WGS AF: 0.0660 AC: 227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.3
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62295889; hg19: chr4-12500221;