rs1483170

Variant names:

• chr8-62195199-G-A
• rs1483170
• ENST00000649904.1:n.667+151C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-62195199-G-A
• chr8-62195199-G-C

Variant summary

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

The ENST00000649904.1(ENSG00000285971):​n.667+151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,018 control chromosomes in the GnomAD database, including 7,992 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 (7992 hom., cov: 32)
• Consequence: ENSG00000285971 ENST00000649904.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

Genes affected

ENSG00000285971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000285971	ENST00000649904.1	n.667+151C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49024 AN: 151900 Hom.: 7982 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.323 AC: 49056 AN: 152018 Hom.: 7992 Cov.: 32 AF XY: 0.325 AC XY: 24180 AN XY: 74298

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.323

Alfa AF: 0.331 Hom.: 3715

Bravo AF: 0.322

Asia WGS AF: 0.374 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.83
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1483170; hg19: chr8-63107758;