rs617022

Variant names:

• chr12-5194396-A-G
• rs617022
• ENST00000789688.1:n.431+22507A>G

Variant summary

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

The ENST00000789688.1(ENSG00000256417):​n.431+22507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,112 control chromosomes in the GnomAD database, including 9,523 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 0.35 (9523 hom., cov: 33)
• Consequence: ENSG00000256417 ENST00000789688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 3 publications found

Genes affected

ENSG00000256417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369617	NR_188065.1	n.771+22507A>G		intron_variant	Intron 4 of 10
LOC105369617	NR_188066.1	n.754+22507A>G		intron_variant	Intron 4 of 9
LOC124902864	XR_007063179.1	n.147+1254T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256417	ENST00000789688.1	n.431+22507A>G		intron_variant	Intron 4 of 8
ENSG00000256417	ENST00000789689.1	n.502+22507A>G		intron_variant	Intron 5 of 11
ENSG00000256417	ENST00000789690.1	n.488+22507A>G		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53377 AN: 151992 Hom.: 9515 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.351 AC: 53402 AN: 152112 Hom.: 9523 Cov.: 33 AF XY: 0.349 AC XY: 25968 AN XY: 74362

African (AFR) AF: 0.291 AC: 12090 AN: 41518

American (AMR) AF: 0.355 AC: 5422 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1870 AN: 5168

South Asian (SAS) AF: 0.404 AC: 1948 AN: 4822

European-Finnish (FIN) AF: 0.336 AC: 3551 AN: 10560

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26051 AN: 67980

Other (OTH) AF: 0.361 AC: 760 AN: 2106

Alfa AF: 0.364 Hom.: 3986

Bravo AF: 0.351

Asia WGS AF: 0.397 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.037
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs617022; hg19: chr12-5303562;