rs13431982

Positions:

• chr2-48205782-T-C
• chr2-48205782-T-G

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.57-25324A>G 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 0.183 in 152,064 control chromosomes in the GnomAD database, including 3,634 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 0.18 (3634 hom., cov: 32)
• Consequence: ENST00000447571.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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
	ENST00000447571.5	n.57-25324A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000651429.1	n.169-40848A>G		intron_variant, non_coding_transcript_variant
	ENST00000650704.1	n.290+37687A>G		intron_variant, non_coding_transcript_variant
	ENST00000658896.1	n.187-40848A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27714 AN: 151946 Hom.: 3620 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.183 AC: 27764 AN: 152064 Hom.: 3634 Cov.: 32 AF XY: 0.179 AC XY: 13304 AN XY: 74358

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.154

Alfa AF: 0.116 Hom.: 535

Bravo AF: 0.188

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.017
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13431982; hg19: chr2-48432921;