17-77948568-G-A

Variant names:

• chr17-77948568-G-A
• rs16970672
• ENST00000722557.1:n.244+201C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000722557.1(ENSG00000294294):​n.244+201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,976 control chromosomes in the GnomAD database, including 8,251 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 0.33 (8251 hom., cov: 32)
• Consequence: ENSG00000294294 ENST00000722557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 11 publications found

Genes affected

ENSG00000294294 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722557.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294294	ENST00000722557.1		n.244+201C>T		intron	N/A
	ENSG00000294294	ENST00000722558.1		n.248+201C>T		intron	N/A
	ENSG00000294294	ENST00000722559.1		n.228+201C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49581 AN: 151858 Hom.: 8247 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.327 AC: 49632 AN: 151976 Hom.: 8251 Cov.: 32 AF XY: 0.330 AC XY: 24501 AN XY: 74300

African (AFR) AF: 0.357 AC: 14781 AN: 41444

American (AMR) AF: 0.344 AC: 5256 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 966 AN: 3472

East Asian (EAS) AF: 0.413 AC: 2137 AN: 5176

South Asian (SAS) AF: 0.378 AC: 1818 AN: 4808

European-Finnish (FIN) AF: 0.302 AC: 3185 AN: 10556

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20224 AN: 67936

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.305 Hom.: 21981

Bravo AF: 0.335

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.061
DANN	Benign	0.67
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs16970672; hg19: chr17-75944650; COSMIC: COSV107162220;