rs2251316

Positions:

• chr4-174537138-C-A
• chr4-174537138-C-T

Variant summary

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

The ENST00000515178.1(ENSG00000293043):​n.1145-548G>T 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 0.323 in 151,878 control chromosomes in the GnomAD database, including 8,170 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 0.32 (8170 hom., cov: 32)
• Consequence: ENST00000515178.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377548	XR_007058487.1	n.6334+257C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515178.1	n.1145-548G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000664316.1	n.478-994C>A		intron_variant, non_coding_transcript_variant
	ENST00000507483.1	n.242+257C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48961 AN: 151760 Hom.: 8160 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.323 AC: 48996 AN: 151878 Hom.: 8170 Cov.: 32 AF XY: 0.317 AC XY: 23539 AN XY: 74210

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.288

Alfa AF: 0.294 Hom.: 9192

Bravo AF: 0.328

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251316; hg19: chr4-175458289;