17-78350215-T-G

Variant names:

• chr17-78350215-T-G
• rs7216115
• ENST00000794841.1:n.139-4612A>C

Variant summary

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

The ENST00000794841.1(ENSG00000303469):​n.139-4612A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 152,208 control chromosomes in the GnomAD database, including 300 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 0.057 (300 hom., cov: 31)
• Consequence: ENSG00000303469 ENST00000794841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 1 publications found

Genes affected

ENSG00000303469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 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
ENSG00000303469	ENST00000794841.1	n.139-4612A>C		intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794842.1	n.135+3188A>C		intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794843.1	n.212+2221A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8615 AN: 152090 Hom.: 300 Cov.: 31

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0370

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0567 AC: 8625 AN: 152208 Hom.: 300 Cov.: 31 AF XY: 0.0563 AC XY: 4187 AN XY: 74404

African (AFR) AF: 0.0483 AC: 2005 AN: 41532

American (AMR) AF: 0.0370 AC: 565 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3472

East Asian (EAS) AF: 0.0608 AC: 315 AN: 5180

South Asian (SAS) AF: 0.113 AC: 544 AN: 4818

European-Finnish (FIN) AF: 0.0447 AC: 474 AN: 10600

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4350 AN: 67996

Other (OTH) AF: 0.0586 AC: 124 AN: 2116

Alfa AF: 0.0260 Hom.: 18

Bravo AF: 0.0543

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7216115; hg19: chr17-76346296;