rs6565624

Positions:

• chr17-81710720-T-C
• chr17-81710720-T-G

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/exons	MANE	Protein	UniProt
		n.81710720T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000262660	ENST00000571730.1	c.570+3507T>C		intron_variant		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;