rs1417032

chr10-6970500-T-C

Variant summary

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

The ENST00000664549.1(ENSG00000287277):n.273-35092A>G 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 0.575 in 152,052 control chromosomes in the GnomAD database, including 25,501 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 0.58 (25501 hom., cov: 33)
• Consequence: ENST00000664549.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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 (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376387	XR_007062046.1	n.446-35092A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664549.1	n.273-35092A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87397 AN: 151934 Hom.: 25496 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.575 AC: 87436 AN: 152052 Hom.: 25501 Cov.: 33 AF XY: 0.568 AC XY: 42182 AN XY: 74326

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.602

Alfa AF: 0.623 Hom.: 60930

Bravo AF: 0.573

Asia WGS AF: 0.404 AC: 1408 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	9.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417032; hg19: chr10-7012462;