chr17-77705615-T-C

Variant names:

• chr17-77705615-T-C
• rs9906155
• ENST00000715849.1:n.126-23987T>C

Variant summary

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

The ENST00000715849.1(ENSG00000267506):​n.126-23987T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,044 control chromosomes in the GnomAD database, including 221 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 0.049 (221 hom., cov: 32)
• Consequence: ENSG00000267506 ENST00000715849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 9 publications found

Genes affected

ENSG00000267506 (HGNC:58772):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715849.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267506	ENST00000715849.1		n.126-23987T>C		intron	N/A
	ENSG00000267506	ENST00000715851.1		n.585-1418T>C		intron	N/A
	ENSG00000267506	ENST00000715858.1		n.70+20251T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7403 AN: 151928 Hom.: 217 Cov.: 32

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0488 AC: 7425 AN: 152044 Hom.: 221 Cov.: 32 AF XY: 0.0469 AC XY: 3484 AN XY: 74298

African (AFR) AF: 0.0634 AC: 2630 AN: 41464

American (AMR) AF: 0.0300 AC: 459 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.0526 AC: 272 AN: 5168

South Asian (SAS) AF: 0.0428 AC: 206 AN: 4812

European-Finnish (FIN) AF: 0.0165 AC: 174 AN: 10544

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

European-Non Finnish (NFE) AF: 0.0506 AC: 3442 AN: 67986

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.0504 Hom.: 78

Bravo AF: 0.0501

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.70

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9906155;

hg19: chr17-75701697;