rs7097872

Positions:

• chr10-102846879-C-T

Variant summary

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

The ENST00000631443.1(ENSG00000282772):​n.382-938G>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 0.406 in 151,992 control chromosomes in the GnomAD database, including 12,681 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 0.41 (12681 hom., cov: 32)
• Consequence: ENST00000631443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000631443.1	n.382-938G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000440461.3	n.259-576G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000629474.2	n.382-576G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000632794.1	n.358-738G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61595 AN: 151874 Hom.: 12666 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.406 AC: 61653 AN: 151992 Hom.: 12681 Cov.: 32 AF XY: 0.404 AC XY: 30016 AN XY: 74302

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.411

Alfa AF: 0.418 Hom.: 1675

Bravo AF: 0.406

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.1
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7097872; hg19: chr10-104606636;