rs17019336

chr4-144412457-T-A

Variant summary

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

The XR_939273.3(LOC105377462):n.240+3446A>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 0.18 in 152,142 control chromosomes in the GnomAD database, including 3,153 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 0.18 (3153 hom., cov: 32)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377462	XR_939273.3	n.240+3446A>T		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.314+3446A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648340.1	n.214+3446A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27399 AN: 152024 Hom.: 3156 Cov.: 32

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.180 AC: 27393 AN: 152142 Hom.: 3153 Cov.: 32 AF XY: 0.180 AC XY: 13368 AN XY: 74392

Gnomad4 AFR AF: 0.0435

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.0879

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.208

Alfa AF: 0.199 Hom.: 428

Bravo AF: 0.180

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	8.4
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17019336; hg19: chr4-145333609;