10-44593605-A-G

Position:

• chr10-44593605-A-G

Variant summary

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

The ENST00000456722.1(ENSG00000234580):​n.156-1821T>C 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 0.485 in 151,746 control chromosomes in the GnomAD database, including 18,033 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 0.48 (18033 hom., cov: 31)
• Consequence: ENST00000456722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902534	XR_007062358.1	n.167-1821T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000456722.1	n.156-1821T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73437 AN: 151628 Hom.: 17999 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.485 AC: 73531 AN: 151746 Hom.: 18033 Cov.: 31 AF XY: 0.488 AC XY: 36205 AN XY: 74146

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.476

Alfa AF: 0.477 Hom.: 4074

Bravo AF: 0.484

Asia WGS AF: 0.558 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2061971; hg19: chr10-45089053;