7-12897630-C-G

Variant names:

• chr7-12897630-C-G
• rs17166499
• ENST00000638964.1:n.484+94898C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638964.1(ENSG00000229618):​n.484+94898C>G 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 151,982 control chromosomes in the GnomAD database, including 2,071 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 (2071 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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
ENSG00000229618	ENST00000638964.1	n.484+94898C>G		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.483+139314C>G		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20124 AN: 151864 Hom.: 2072 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.133 AC: 20138 AN: 151982 Hom.: 2071 Cov.: 32 AF XY: 0.131 AC XY: 9704 AN XY: 74302

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0359 Hom.: 22

Bravo AF: 0.138

Asia WGS AF: 0.108 AC: 374 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17166499; hg19: chr7-12937255;