rs7097872

Variant names:

• chr10-102846879-C-T
• rs7097872
• ENST00000440461.3:n.259-576G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631443.1(ENSG00000282772):​n.382-938G>A variant causes a intron 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: ENSG00000282772 ENST00000631443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 7 publications found

Genes affected

ENSG00000282772 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631443.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282772	ENST00000440461.3	TSL:5	n.259-576G>A		intron	N/A
	ENSG00000282772	ENST00000629474.2	TSL:5	n.382-576G>A		intron	N/A
	ENSG00000282772	ENST00000631443.1	TSL:4	n.382-938G>A		intron	N/A

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

African (AFR) AF: 0.375 AC: 15529 AN: 41440

American (AMR) AF: 0.403 AC: 6159 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3472

East Asian (EAS) AF: 0.563 AC: 2911 AN: 5168

South Asian (SAS) AF: 0.467 AC: 2249 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3784 AN: 10548

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28325 AN: 67964

Other (OTH) AF: 0.411 AC: 866 AN: 2106

Alfa AF: 0.416 Hom.: 1733

Bravo AF: 0.406

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.1
DANN	Benign	0.24
PhyloP100		-0.70

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7097872;

hg19: chr10-104606636;