5-126197437-C-T

Position:

• chr5-126197437-C-T

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.77-2208G>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 0.26 in 141,280 control chromosomes in the GnomAD database, including 4,681 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 (4681 hom., cov: 27)
• Consequence: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1620-99276G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651847.1	n.77-2208G>A		intron_variant, non_coding_transcript_variant
	ENST00000450613.2	n.71+82294G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 36749 AN: 141168 Hom.: 4680 Cov.: 27

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.260 AC: 36766 AN: 141280 Hom.: 4681 Cov.: 27 AF XY: 0.261 AC XY: 17733 AN XY: 68070

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.267

Alfa AF: 0.258 Hom.: 10213

Bravo AF: 0.248

Asia WGS AF: 0.154 AC: 531 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17584191; hg19: chr5-125533130;