chr17-81710720-T-C

Variant names:

• chr17-81710720-T-C
• rs6565624
• ENST00000571730.1:c.570+3507T>C

Variant summary

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

The ENST00000571730.1(ENSG00000262660):​c.570+3507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,174 control chromosomes in the GnomAD database, including 5,159 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 0.25 (5159 hom., cov: 33)
• Consequence: ENSG00000262660 ENST00000571730.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

Genes affected

ENSG00000262660 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000262660	ENST00000571730.1	c.570+3507T>C		intron_variant	Intron 5 of 14	2		ENSP00000461324.1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38131 AN: 152056 Hom.: 5145 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.251 AC: 38186 AN: 152174 Hom.: 5159 Cov.: 33 AF XY: 0.247 AC XY: 18362 AN XY: 74420

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.253

Alfa AF: 0.223 Hom.: 5729

Bravo AF: 0.258

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs6565624; hg19: chr17-79677750;