7-106771412-T-C

Variant names:

• chr7-106771412-T-C
• rs17477177
• ENST00000789608.1:n.109+4264A>G

Variant summary

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

The ENST00000789608.1(ENSG00000243797):​n.109+4264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,748 control chromosomes in the GnomAD database, including 2,722 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 0.17 (2722 hom., cov: 30)
• Consequence: ENSG00000243797 ENST00000789608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 47 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 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
ENSG00000243797	ENST00000789608.1	n.109+4264A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26330 AN: 151632 Hom.: 2723 Cov.: 30

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.174 AC: 26335 AN: 151748 Hom.: 2722 Cov.: 30 AF XY: 0.180 AC XY: 13339 AN XY: 74120

African (AFR) AF: 0.0733 AC: 3041 AN: 41460

American (AMR) AF: 0.162 AC: 2468 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3464

East Asian (EAS) AF: 0.135 AC: 695 AN: 5162

South Asian (SAS) AF: 0.299 AC: 1435 AN: 4798

European-Finnish (FIN) AF: 0.322 AC: 3365 AN: 10462

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13957 AN: 67900

Other (OTH) AF: 0.189 AC: 398 AN: 2102

Alfa AF: 0.190 Hom.: 11792

Bravo AF: 0.153

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs17477177; hg19: chr7-106411858;