rs2394075

Positions:

• chr10-64521033-T-A

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.734-170409T>A 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 0.527 in 151,822 control chromosomes in the GnomAD database, including 21,871 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 0.53 (21871 hom., cov: 30)
• Consequence: ENST00000654191.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902439	XR_007062161.1	n.715-170409T>A		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062160.1	n.713-170409T>A		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062165.1	n.270-170409T>A		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062166.1	n.433-170409T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654191.1	n.734-170409T>A		intron_variant, non_coding_transcript_variant
	ENST00000660795.1	n.580-170409T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80026 AN: 151702 Hom.: 21858 Cov.: 30

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.527 AC: 80067 AN: 151822 Hom.: 21871 Cov.: 30 AF XY: 0.520 AC XY: 38556 AN XY: 74180

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.499

Alfa AF: 0.563 Hom.: 3031

Bravo AF: 0.516

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2394075; hg19: chr10-66280790;