rs17079195

Variant names:

• chr18-68470657-A-C
• rs17079195
• ENST00000661028.2:n.581+24222T>G

Your query was ambiguous. Multiple possible variants found:

• chr18-68470657-A-C
• chr18-68470657-A-T

Variant summary

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

The ENST00000661028.2(ENSG00000287907):​n.581+24222T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,180 control chromosomes in the GnomAD database, including 2,361 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 0.16 (2361 hom., cov: 32)
• Consequence: ENSG00000287907 ENST00000661028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 6 publications found

Genes affected

ENSG00000287907 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287907	ENST00000661028.2	n.581+24222T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24915 AN: 152062 Hom.: 2354 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.164 AC: 24939 AN: 152180 Hom.: 2361 Cov.: 32 AF XY: 0.168 AC XY: 12505 AN XY: 74384

African (AFR) AF: 0.210 AC: 8709 AN: 41534

American (AMR) AF: 0.137 AC: 2095 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3466

East Asian (EAS) AF: 0.407 AC: 2099 AN: 5152

South Asian (SAS) AF: 0.174 AC: 839 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10590

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8134 AN: 68004

Other (OTH) AF: 0.169 AC: 356 AN: 2110

Alfa AF: 0.144 Hom.: 6113

Bravo AF: 0.167

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.62
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs17079195; hg19: chr18-66137894;