rs7655116

Variant names:

• chr4-157712200-T-G
• rs7655116
• ENST00000652341.2:n.456-34867A>C

Variant summary

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

The ENST00000652341.2(ENSG00000287226):​n.456-34867A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0282 in 152,024 control chromosomes in the GnomAD database, including 245 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 0.028 (245 hom., cov: 32)
• Consequence: ENSG00000287226 ENST00000652341.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 1 publications found

Genes affected

ENSG00000287226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287226	ENST00000652341.2	n.456-34867A>C		intron_variant	Intron 1 of 2
ENSG00000287226	ENST00000809875.1	n.70-34867A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0281 AC: 4275 AN: 151908 Hom.: 243 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00911

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0282 AC: 4284 AN: 152024 Hom.: 245 Cov.: 32 AF XY: 0.0267 AC XY: 1984 AN XY: 74312

African (AFR) AF: 0.0983 AC: 4077 AN: 41484

American (AMR) AF: 0.00910 AC: 139 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 67860

Other (OTH) AF: 0.0166 AC: 35 AN: 2112

Alfa AF: 0.0264 Hom.: 29

Bravo AF: 0.0332

Asia WGS AF: 0.00609 AC: 21 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7655116; hg19: chr4-158633352;