rs10517374

chr4-36365647-T-Achr4-36365647-T-C

Variant summary

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

The ENST00000504344.1(ENSG00000251438):n.330+26434A>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 0.059 in 152,196 control chromosomes in the GnomAD database, including 548 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 0.059 (548 hom., cov: 32)
• Consequence: ENST00000504344.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374399	XR_925195.3	n.1668-175T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504344.1	n.330+26434A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8943 AN: 152078 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0590 AC: 8979 AN: 152196 Hom.: 548 Cov.: 32 AF XY: 0.0626 AC XY: 4660 AN XY: 74416

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0150

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0370 Hom.: 27

Bravo AF: 0.0702

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	13
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517374; hg19: chr4-36367269;