rs17459015

Variant names:

• chr6-104369900-T-C
• rs17459015
• ENST00000806122.1:n.73-31216A>G

Variant summary

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

The ENST00000806122.1(ENSG00000304752):​n.73-31216A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,196 control chromosomes in the GnomAD database, including 1,905 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 0.14 (1905 hom., cov: 32)
• Consequence: ENSG00000304752 ENST00000806122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 3 publications found

Genes affected

ENSG00000304752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806122.1. 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
	ENSG00000304752	ENST00000806122.1		n.73-31216A>G		intron	N/A
	ENSG00000304752	ENST00000806123.1		n.159-31216A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21063 AN: 152078 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.138 AC: 21059 AN: 152196 Hom.: 1905 Cov.: 32 AF XY: 0.138 AC XY: 10285 AN XY: 74416

African (AFR) AF: 0.0330 AC: 1371 AN: 41540

American (AMR) AF: 0.119 AC: 1824 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.109 AC: 566 AN: 5172

South Asian (SAS) AF: 0.197 AC: 948 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2243 AN: 10580

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13136 AN: 67994

Other (OTH) AF: 0.111 AC: 234 AN: 2110

Alfa AF: 0.168 Hom.: 5665

Bravo AF: 0.124

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		-0.38

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: rs17459015;

hg19: chr6-104817775;

COSMIC: COSV60261965;