2-48948101-T-G

Variant names:

• chr2-48948101-T-G
• rs17500266
• ENST00000634588.1:n.492+1696T>G

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.492+1696T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,046 control chromosomes in the GnomAD database, including 17,833 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 0.48 (17833 hom., cov: 32)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 1 publications found

Genes affected

MIR548BAHG (HGNC:58158):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR548BAHG	ENST00000634588.1	TSL:5	n.492+1696T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72838 AN: 151928 Hom.: 17830 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.479 AC: 72864 AN: 152046 Hom.: 17833 Cov.: 32 AF XY: 0.482 AC XY: 35808 AN XY: 74334

African (AFR) AF: 0.381 AC: 15790 AN: 41440

American (AMR) AF: 0.512 AC: 7821 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1639 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2554 AN: 5170

South Asian (SAS) AF: 0.534 AC: 2567 AN: 4808

European-Finnish (FIN) AF: 0.537 AC: 5678 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.519 AC: 35309 AN: 67978

Other (OTH) AF: 0.488 AC: 1032 AN: 2114

Alfa AF: 0.502 Hom.: 78214

Bravo AF: 0.469

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs17500266; hg19: chr2-49175240;