rs17041904

Positions:

• chr3-16127170-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124906217 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906217	XR_007095836.1	n.789G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702609.1	n.197-10221C>T		intron_variant, non_coding_transcript_variant
	ENST00000691919.2	n.240-10221C>T		intron_variant, non_coding_transcript_variant
	ENST00000702385.1	n.230-10221C>T		intron_variant, non_coding_transcript_variant
	ENST00000702645.1	n.549-10221C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.127

Alfa AF: 0.109 Hom.: 991

Bravo AF: 0.150

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17041904; hg19: chr3-16168677;