rs4968779

Positions:

• chr17-63455210-A-G
• chr17-63455210-A-T

Variant summary

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

The ENST00000582741.1(ENSG00000265971):​n.218A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,112 control chromosomes in the GnomAD database, including 26,662 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 0.58 (26660 hom., cov: 32)
  • Exomes 𝑓: 0.64 (2 hom.)
• Consequence: ENSG00000265971 ENST00000582741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

ENSG00000265971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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	Protein	UniProt
		n.63455210A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000265971	ENST00000582741.1	n.218A>G		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87447 AN: 151980 Hom.: 26610 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.524

GnomAD4 exome AF: 0.643 AC: 9 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.625 AC XY: 5 AN XY: 8

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.576 AC: 87557 AN: 152098 Hom.: 26660 Cov.: 32 AF XY: 0.570 AC XY: 42373 AN XY: 74372

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.529

Alfa AF: 0.519 Hom.: 25184

Bravo AF: 0.572

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4968779; hg19: chr17-61532571;