rs1079866

Variant names:

• chr7-41430495-C-G
• rs1079866
• ENST00000813847.1:n.278-9310G>C

Variant summary

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

The ENST00000813847.1(ENSG00000305895):​n.278-9310G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,038 control chromosomes in the GnomAD database, including 1,368 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 0.13 (1368 hom., cov: 31)
• Consequence: ENSG00000305895 ENST00000813847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 37 publications found

Genes affected

ENSG00000305895 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813847.1. 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
	ENSG00000305895	ENST00000813847.1		n.278-9310G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19217 AN: 151920 Hom.: 1367 Cov.: 31

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.126 AC: 19218 AN: 152038 Hom.: 1368 Cov.: 31 AF XY: 0.128 AC XY: 9475 AN XY: 74290

African (AFR) AF: 0.0875 AC: 3628 AN: 41468

American (AMR) AF: 0.107 AC: 1633 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1130 AN: 5114

South Asian (SAS) AF: 0.134 AC: 647 AN: 4814

European-Finnish (FIN) AF: 0.178 AC: 1880 AN: 10558

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9225 AN: 68008

Other (OTH) AF: 0.125 AC: 265 AN: 2112

Alfa AF: 0.139 Hom.: 882

Bravo AF: 0.119

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.063
DANN	Benign	0.69
PhyloP100		-2.4

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: rs1079866;

hg19: chr7-41470093;