17-63455210-A-G

Variant names:

• chr17-63455210-A-G
• rs4968779
• ENST00000582741.1:n.218A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000265971 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582741.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265971	ENST00000582741.1	TSL:4	n.218A>G		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.833 AC: 5 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.771 AC: 31983 AN: 41502

American (AMR) AF: 0.464 AC: 7083 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3468

East Asian (EAS) AF: 0.176 AC: 909 AN: 5166

South Asian (SAS) AF: 0.518 AC: 2497 AN: 4818

European-Finnish (FIN) AF: 0.556 AC: 5886 AN: 10584

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35687 AN: 67964

Other (OTH) AF: 0.529 AC: 1116 AN: 2110

Alfa AF: 0.533 Hom.: 74872

Bravo AF: 0.572

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.47
PhyloP100		-0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4968779;

hg19: chr17-61532571;