rs10495950

Variant names:

• chr2-48207625-T-G
• rs10495950
• ENST00000447571.5:n.57-27167A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447571.5(ENSG00000230773):​n.57-27167A>C variant causes a intron 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: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 8 publications found

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230773	ENST00000447571.5	TSL:1	n.57-27167A>C		intron	N/A
	ENSG00000230773	ENST00000650704.1		n.290+35844A>C		intron	N/A
	ENSG00000230773	ENST00000651429.1		n.169-42691A>C		intron	N/A

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

African (AFR) AF: 0.301 AC: 12505 AN: 41476

American (AMR) AF: 0.0984 AC: 1506 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5194

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8771 AN: 68006

Other (OTH) AF: 0.140 AC: 297 AN: 2116

Alfa AF: 0.130 Hom.: 2190

Bravo AF: 0.167

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.62
PhyloP100		-0.085

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10495950;

hg19: chr2-48434764;