rs1487971

Variant names:

• chr17-30245735-C-T
• rs1487971
• ENST00000577420.2:n.260-6339C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577420.2(ENSG00000266120):​n.260-6339C>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 ENST00000577420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 16 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000577420.2	n.260-6339C>T		intron_variant	Intron 1 of 2	3
ENSG00000266120	ENST00000724730.1	n.258-4052C>T		intron_variant	Intron 1 of 1
ENSG00000266120	ENST00000724731.1	n.721-13C>T		intron_variant	Intron 3 of 4
ENSG00000266120	ENST00000724732.1	n.171-1019C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.613 AC: 25374 AN: 41388

American (AMR) AF: 0.412 AC: 6297 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1073 AN: 5158

South Asian (SAS) AF: 0.362 AC: 1740 AN: 4806

European-Finnish (FIN) AF: 0.405 AC: 4278 AN: 10558

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25929 AN: 67936

Other (OTH) AF: 0.420 AC: 888 AN: 2112

Alfa AF: 0.404 Hom.: 6983

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1487971; hg19: chr17-28572753;