rs9257616

Variant names:

• chr6-29212944-G-A
• rs9257616
• ENST00000642091.1:n.44+15G>A

Your query was ambiguous. Multiple possible variants found:

• 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 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: ENSG00000290478 ENST00000642091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

ENSG00000290478 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290478	ENST00000642091.1	n.44+15G>A		intron_variant	Intron 1 of 1

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;