rs17041904

Variant names:

• chr3-16127170-C-T
• rs17041904
• XR_007095836.1:n.789G>A

Variant summary

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

The XR_007095836.1(LOC124906217):​n.789G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,194 control chromosomes in the GnomAD database, including 1,992 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 (1992 hom., cov: 32)
• Consequence: LOC124906217 XR_007095836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697
• Publications: 4 publications found

Genes affected

LOC124906217 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691919.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287042	ENST00000691919.3		n.259-10221C>T		intron	N/A
	ENSG00000287042	ENST00000702385.2		n.293-10221C>T		intron	N/A
	ENSG00000287042	ENST00000702609.2		n.217-10221C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21172 AN: 152076 Hom.: 1990 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.139 AC: 21193 AN: 152194 Hom.: 1992 Cov.: 32 AF XY: 0.142 AC XY: 10531 AN XY: 74416

African (AFR) AF: 0.183 AC: 7612 AN: 41516

American (AMR) AF: 0.160 AC: 2448 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2495 AN: 5172

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4818

European-Finnish (FIN) AF: 0.0587 AC: 623 AN: 10614

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6328 AN: 68000

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.113 Hom.: 1424

Bravo AF: 0.150

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.4
DANN	Benign	0.49
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs17041904; hg19: chr3-16168677;