17-63502251-C-T

Variant names:

• chr17-63502251-C-T
• rs7221678
• ENST00000577647.2:n.1970-4805C>T

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.1970-4805C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,642 control chromosomes in the GnomAD database, including 24,086 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 0.56 (24086 hom., cov: 32)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 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
ENSG00000264813	ENST00000577647.2	n.1970-4805C>T		intron_variant	Intron 13 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84237 AN: 151524 Hom.: 24026 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.556 AC: 84357 AN: 151642 Hom.: 24086 Cov.: 32 AF XY: 0.557 AC XY: 41253 AN XY: 74054

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.504

Alfa AF: 0.400 Hom.: 1105

Bravo AF: 0.561

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7221678; hg19: chr17-61579612;