rs9257616

Positions:

• chr6-29212944-G-A
• chr6-29212944-G-C
• chr6-29212944-G-T

Variant summary

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

The ENST00000642091.1(ENSG00000290478):​n.44+15G>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 0.349 in 152,044 control chromosomes in the GnomAD database, including 11,496 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 0.35 (11496 hom., cov: 31)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENST00000642091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 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
	ENST00000642091.1	n.44+15G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52978 AN: 151920 Hom.: 11481 Cov.: 31

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.339

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.349 AC: 52992 AN: 152038 Hom.: 11496 Cov.: 31 AF XY: 0.354 AC XY: 26274 AN XY: 74296

Gnomad4 AFR AF: 0.0851

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.345

Alfa AF: 0.410 Hom.: 5112

Bravo AF: 0.322

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9257616; hg19: chr6-29180721;