rs12657996

Variant names:

• chr5-159477305-G-A
• rs12657996
• ENST00000636261.1:n.367+53175G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-159477305-G-A
• chr5-159477305-G-C

Variant summary

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

The ENST00000636261.1(ENSG00000249738):​n.367+53175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,032 control chromosomes in the GnomAD database, including 6,286 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 0.28 (6286 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000636261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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
ENSG00000249738	ENST00000636261.1	n.367+53175G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42296 AN: 151912 Hom.: 6278 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.279 AC: 42342 AN: 152032 Hom.: 6286 Cov.: 32 AF XY: 0.280 AC XY: 20780 AN XY: 74310

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.262

Alfa AF: 0.237 Hom.: 7661

Bravo AF: 0.281

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12657996; hg19: chr5-158904313;