rs1299048

Positions:

• chr5-162800705-T-A
• chr5-162800705-T-G

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.911-4786A>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 0.472 in 151,936 control chromosomes in the GnomAD database, including 17,096 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 0.47 (17096 hom., cov: 32)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646617.1	n.911-4786A>T		intron_variant, non_coding_transcript_variant
	ENST00000660514.1	n.476-4786A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71626 AN: 151818 Hom.: 17078 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.472 AC: 71682 AN: 151936 Hom.: 17096 Cov.: 32 AF XY: 0.477 AC XY: 35393 AN XY: 74254

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.455

Alfa AF: 0.475 Hom.: 2139

Bravo AF: 0.469

Asia WGS AF: 0.598 AC: 2077 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1299048; hg19: chr5-162227711;