rs17165506

Variant names:

• chr7-12013744-A-G
• rs17165506
• ENST00000775347.1:n.290+80909T>C

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.290+80909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,232 control chromosomes in the GnomAD database, including 1,427 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 (1427 hom., cov: 32)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 2 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901589	XR_007060211.1	n.85+80909T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300984	ENST00000775347.1	n.290+80909T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19017 AN: 152114 Hom.: 1422 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.125 AC: 19045 AN: 152232 Hom.: 1427 Cov.: 32 AF XY: 0.128 AC XY: 9519 AN XY: 74430

African (AFR) AF: 0.0635 AC: 2638 AN: 41560

American (AMR) AF: 0.205 AC: 3133 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5180

South Asian (SAS) AF: 0.163 AC: 785 AN: 4828

European-Finnish (FIN) AF: 0.117 AC: 1238 AN: 10590

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8864 AN: 68002

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.129 Hom.: 302

Bravo AF: 0.132

Asia WGS AF: 0.157 AC: 542 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.91
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs17165506; hg19: chr7-12053370;