rs12938916

Variant names:

• chr17-57788926-G-A
• rs12938916
• ENST00000580960.1:n.255-16730C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000580960.1(ENSG00000265542):​n.255-16730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,220 control chromosomes in the GnomAD database, including 282 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 0.055 (282 hom., cov: 32)
• Consequence: ENSG00000265542 ENST00000580960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

Genes affected

ENSG00000265542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 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
ENSG00000265542	ENST00000580960.1	n.255-16730C>T		intron_variant	Intron 1 of 1	2
ENSG00000265542	ENST00000581805.5	n.222-16730C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8301 AN: 152102 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0547 AC: 8319 AN: 152220 Hom.: 282 Cov.: 32 AF XY: 0.0566 AC XY: 4216 AN XY: 74426

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.0536

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0537

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0538 Hom.: 249

Bravo AF: 0.0515

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12938916; hg19: chr17-55866287;