rs73317122

Variant names:

• chr17-26993863-G-T
• rs73317122
• ENST00000580686.2:n.673-2250C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000580686.2(ENSG00000264734):​n.673-2250C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.44 (0 hom., cov: 36)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000264734 ENST00000580686.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44
• Publications: 2 publications found

Genes affected

ENSG00000264734 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580686.2. 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
	ENSG00000264734	ENST00000580686.2	TSL:3	n.673-2250C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 34377 AN: 77722 Hom.: 0 Cov.: 36

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.434

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.442 AC: 34398 AN: 77776 Hom.: 0 Cov.: 36 AF XY: 0.441 AC XY: 17071 AN XY: 38744

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.449 AC: 9706 AN: 21640

American (AMR) AF: 0.421 AC: 3129 AN: 7440

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 761 AN: 1664

East Asian (EAS) AF: 0.389 AC: 925 AN: 2378

South Asian (SAS) AF: 0.409 AC: 965 AN: 2358

European-Finnish (FIN) AF: 0.414 AC: 2325 AN: 5610

Middle Eastern (MID) AF: 0.287 AC: 27 AN: 94

European-Non Finnish (NFE) AF: 0.453 AC: 15853 AN: 34992

Other (OTH) AF: 0.433 AC: 491 AN: 1134

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.747 Hom.: 6613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.52
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs73317122; hg19: chr17-25320889; COSMIC: COSV73869410;