rs12657996

Positions:

• 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, non coding transcript 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: ENST00000636261.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636261.1	n.367+53175G>A		intron_variant, non_coding_transcript_variant		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;