rs10495950

chr2-48207625-T-G

Variant summary

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

The ENST00000447571.5(ENSG00000230773):n.57-27167A>C 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 0.164 in 152,184 control chromosomes in the GnomAD database, including 2,763 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 0.16 (2763 hom., cov: 32)
• Consequence: ENST00000447571.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000447571.5	n.57-27167A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000651429.1	n.169-42691A>C		intron_variant, non_coding_transcript_variant
	ENST00000650704.1	n.290+35844A>C		intron_variant, non_coding_transcript_variant
	ENST00000658896.1	n.187-42691A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24918 AN: 152066 Hom.: 2755 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.164 AC: 24958 AN: 152184 Hom.: 2763 Cov.: 32 AF XY: 0.160 AC XY: 11937 AN XY: 74414

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.140

Alfa AF: 0.124 Hom.: 1526

Bravo AF: 0.167

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495950; hg19: chr2-48434764;