rs6505165

Positions:

• chr17-30247831-T-C

Variant summary

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

The ENST00000577420.1(ENSG00000266120):​n.61-4243T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,046 control chromosomes in the GnomAD database, including 23,604 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 0.53 (23604 hom., cov: 31)
• Consequence: ENST00000577420.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371720	XR_001752824.2	n.892-1956T>C		intron_variant, non_coding_transcript_variant
LOC105371720	XR_007065695.1	n.756-1956T>C		intron_variant, non_coding_transcript_variant
LOC105371720	XR_007065698.1	n.756-4243T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000577420.1	n.61-4243T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81006 AN: 151928 Hom.: 23544 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.534 AC: 81131 AN: 152046 Hom.: 23604 Cov.: 31 AF XY: 0.530 AC XY: 39389 AN XY: 74318

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.490

Alfa AF: 0.507 Hom.: 3311

Bravo AF: 0.536

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.048
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6505165; hg19: chr17-28574849;