rs9957708

Variant names:

• chr18-27799426-A-G
• rs9957708
• ENST00000750368.1:n.221-1616T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-27799426-A-G
• chr18-27799426-A-T

Variant summary

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

The ENST00000750368.1(ENSG00000297707):​n.221-1616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,012 control chromosomes in the GnomAD database, including 24,622 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 0.54 (24622 hom., cov: 33)
• Consequence: ENSG00000297707 ENST00000750368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 2 publications found

Genes affected

ENSG00000297707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372042	XR_935323.3	n.696-3495A>G		intron_variant	Intron 3 of 4
LOC105372042	XR_935324.3	n.628-3495A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297707	ENST00000750368.1	n.221-1616T>C		intron_variant	Intron 1 of 4
ENSG00000286426	ENST00000750547.1	n.481-3495A>G		intron_variant	Intron 2 of 3
ENSG00000286426	ENST00000750548.1	n.473-3495A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82511 AN: 151896 Hom.: 24616 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.543 AC: 82531 AN: 152012 Hom.: 24622 Cov.: 33 AF XY: 0.548 AC XY: 40701 AN XY: 74306

African (AFR) AF: 0.283 AC: 11738 AN: 41460

American (AMR) AF: 0.648 AC: 9891 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2413 AN: 5154

South Asian (SAS) AF: 0.580 AC: 2791 AN: 4814

European-Finnish (FIN) AF: 0.698 AC: 7371 AN: 10556

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44299 AN: 67970

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

Alfa AF: 0.590 Hom.: 4844

Bravo AF: 0.526

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.80
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9957708; hg19: chr18-25379390;