rs7071843

Variant names:

• chr10-113351730-T-G
• rs7071843
• ENST00000818152.1:n.270-5291T>G

Variant summary

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

The ENST00000818152.1(ENSG00000306410):​n.270-5291T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,032 control chromosomes in the GnomAD database, including 24,185 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 (24185 hom., cov: 32)
• Consequence: ENSG00000306410 ENST00000818152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 2 publications found

Genes affected

ENSG00000306410 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818152.1. 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
	ENSG00000306410	ENST00000818152.1		n.270-5291T>G		intron	N/A
	ENSG00000306410	ENST00000818153.1		n.125-5291T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81078 AN: 151914 Hom.: 24193 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.533 AC: 81064 AN: 152032 Hom.: 24185 Cov.: 32 AF XY: 0.533 AC XY: 39579 AN XY: 74310

African (AFR) AF: 0.292 AC: 12090 AN: 41444

American (AMR) AF: 0.569 AC: 8702 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3470

East Asian (EAS) AF: 0.152 AC: 784 AN: 5174

South Asian (SAS) AF: 0.383 AC: 1839 AN: 4806

European-Finnish (FIN) AF: 0.710 AC: 7491 AN: 10550

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45891 AN: 67998

Other (OTH) AF: 0.558 AC: 1174 AN: 2104

Alfa AF: 0.603 Hom.: 3774

Bravo AF: 0.514

Asia WGS AF: 0.259 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.35
PhyloP100		0.073

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: rs7071843;

hg19: chr10-115111489;