rs4362772

chr4-144408650-C-Achr4-144408650-C-G

Variant summary

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

The XR_939273.3(LOC105377462):n.240+7253G>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 0.612 in 151,806 control chromosomes in the GnomAD database, including 28,443 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 0.61 (28443 hom., cov: 32)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377462	XR_939273.3	n.240+7253G>T		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.314+7253G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648340.1	n.214+7253G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92839 AN: 151686 Hom.: 28418 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.612 AC: 92913 AN: 151806 Hom.: 28443 Cov.: 32 AF XY: 0.615 AC XY: 45596 AN XY: 74172

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.603

Alfa AF: 0.609 Hom.: 12815

Bravo AF: 0.604

Asia WGS AF: 0.535 AC: 1855 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4362772; hg19: chr4-145329802;