7-81661206-A-G

Variant names:

• chr7-81661206-A-G
• rs7799610
• ENST00000413944.3:n.78+30123T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000413944.3(ENSG00000293394):​n.78+30123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,018 control chromosomes in the GnomAD database, including 51,070 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 0.81 (51070 hom., cov: 31)
• Consequence: ENSG00000293394 ENST00000413944.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 2 publications found

Genes affected

ENSG00000293394 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413944.3. 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
	LOC100128317	NR_126025.1		n.78+30123T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293394	ENST00000413944.3	TSL:1	n.78+30123T>C		intron	N/A
	ENSG00000293394	ENST00000636281.1	TSL:5	n.228+29059T>C		intron	N/A
	ENSG00000293394	ENST00000648981.1		n.150+29059T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122653 AN: 151900 Hom.: 51060 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.807 AC: 122698 AN: 152018 Hom.: 51070 Cov.: 31 AF XY: 0.805 AC XY: 59841 AN XY: 74310

African (AFR) AF: 0.607 AC: 25122 AN: 41410

American (AMR) AF: 0.858 AC: 13095 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3225 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2863 AN: 5154

South Asian (SAS) AF: 0.755 AC: 3633 AN: 4814

European-Finnish (FIN) AF: 0.907 AC: 9593 AN: 10582

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.916 AC: 62313 AN: 68006

Other (OTH) AF: 0.838 AC: 1768 AN: 2110

Alfa AF: 0.887 Hom.: 99677

Bravo AF: 0.795

Asia WGS AF: 0.643 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	13
DANN	Benign	0.97
PhyloP100		0.24

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: rs7799610;

hg19: chr7-81290522;