rs17044137

Positions:

• chr4-111874141-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000679726.1(ENSG00000288691):​n.170+23835T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,010 control chromosomes in the GnomAD database, including 5,260 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 0.26 (5260 hom., cov: 31)
• Consequence: ENST00000679726.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783

Genes affected

(HGNC:):

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377369	XR_939077.3	n.512+23835T>A		intron_variant, non_coding_transcript_variant
LOC105377369	XR_939076.3	n.170+23835T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000679726.1	n.170+23835T>A		intron_variant, non_coding_transcript_variant
LINC02945	ENST00000679735.1	n.188-45091A>T		intron_variant, non_coding_transcript_variant
LINC02945	ENST00000511219.1	n.135-45091A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39100 AN: 151892 Hom.: 5243 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.258 AC: 39155 AN: 152010 Hom.: 5260 Cov.: 31 AF XY: 0.252 AC XY: 18748 AN XY: 74328

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.266

Alfa AF: 0.242 Hom.: 550

Bravo AF: 0.262

Asia WGS AF: 0.149 AC: 525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17044137; hg19: chr4-112795297;