7-35079306-T-C

Variant names:

• chr7-35079306-T-C
• rs3864439
• ENST00000659178.1:n.87-23160T>C

Variant summary

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

The ENST00000659178.1(ENSG00000287249):​n.87-23160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,146 control chromosomes in the GnomAD database, including 1,455 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 (1455 hom., cov: 32)
• Consequence: ENSG00000287249 ENST00000659178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 2 publications found

Genes affected

ENSG00000287249 (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 = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375228	XR_001745162.3	n.137-23160T>C		intron_variant	Intron 1 of 2
LOC105375228	XR_001745164.3	n.7019+1455T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287249	ENST00000659178.1	n.87-23160T>C		intron_variant	Intron 1 of 2
ENSG00000287249	ENST00000784664.1	n.164-23160T>C		intron_variant	Intron 1 of 3
ENSG00000287249	ENST00000784666.1	n.76-23160T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20315 AN: 152028 Hom.: 1455 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0665

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.133 AC: 20306 AN: 152146 Hom.: 1455 Cov.: 32 AF XY: 0.133 AC XY: 9876 AN XY: 74370

African (AFR) AF: 0.110 AC: 4572 AN: 41512

American (AMR) AF: 0.101 AC: 1548 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3472

East Asian (EAS) AF: 0.0661 AC: 343 AN: 5188

South Asian (SAS) AF: 0.124 AC: 595 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10580

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10886 AN: 67986

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.135 Hom.: 213

Bravo AF: 0.127

Asia WGS AF: 0.101 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.48
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs3864439; hg19: chr7-35118918;