rs10495970

Variant names:

• chr2-49264671-G-A
• rs10495970
• ENST00000634588.1:n.493-143531G>A

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.493-143531G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,874 control chromosomes in the GnomAD database, including 5,102 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 0.26 (5102 hom., cov: 32)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 1 publications found

Genes affected

MIR548BAHG (HGNC:58158):

ENSG00000282998 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634588.1. 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
	MIR548BAHG	ENST00000634588.1	TSL:5	n.493-143531G>A		intron	N/A
	ENSG00000282998	ENST00000635306.2	TSL:5	n.408-46043C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38748 AN: 151756 Hom.: 5098 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.255 AC: 38778 AN: 151874 Hom.: 5102 Cov.: 32 AF XY: 0.256 AC XY: 19012 AN XY: 74214

African (AFR) AF: 0.298 AC: 12318 AN: 41378

American (AMR) AF: 0.172 AC: 2625 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1775 AN: 5142

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4812

European-Finnish (FIN) AF: 0.314 AC: 3311 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15968 AN: 67966

Other (OTH) AF: 0.257 AC: 541 AN: 2106

Alfa AF: 0.243 Hom.: 3111

Bravo AF: 0.250

Asia WGS AF: 0.280 AC: 974 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.038

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: rs10495970;

hg19: chr2-49491810;