rs1487971

Variant names:

• chr17-30245735-C-T
• rs1487971
• ENST00000577420.1:n.61-6339C>T

Variant summary

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

The ENST00000577420.1(ENSG00000266120):​n.61-6339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,914 control chromosomes in the GnomAD database, including 15,915 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 0.44 (15915 hom., cov: 31)
• Consequence: ENSG00000266120 ENST00000577420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.892-4052C>T		intron_variant	Intron 3 of 3
LOC105371720	XR_007065695.1	n.756-4052C>T		intron_variant	Intron 2 of 2
LOC105371720	XR_007065696.1	n.756-13C>T		intron_variant	Intron 2 of 2
LOC105371720	XR_007065698.1	n.756-6339C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000577420.1	n.61-6339C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67097 AN: 151798 Hom.: 15863 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.442 AC: 67212 AN: 151914 Hom.: 15915 Cov.: 31 AF XY: 0.438 AC XY: 32543 AN XY: 74238

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.420

Alfa AF: 0.404 Hom.: 6257

Bravo AF: 0.448

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487971; hg19: chr17-28572753;