2-48944910-C-T

Variant names:

• chr2-48944910-C-T
• rs6739570
• ENST00000634588.1:n.303-1306C>T

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.303-1306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,930 control chromosomes in the GnomAD database, including 1,349 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 0.11 (1349 hom., cov: 32)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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.303-1306C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16738 AN: 151812 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.0963

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.111 AC: 16789 AN: 151930 Hom.: 1349 Cov.: 32 AF XY: 0.112 AC XY: 8317 AN XY: 74236

African (AFR) AF: 0.208 AC: 8609 AN: 41404

American (AMR) AF: 0.115 AC: 1757 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1319 AN: 5160

South Asian (SAS) AF: 0.0826 AC: 398 AN: 4816

European-Finnish (FIN) AF: 0.0963 AC: 1014 AN: 10534

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0488 AC: 3319 AN: 67984

Other (OTH) AF: 0.0971 AC: 205 AN: 2112

Alfa AF: 0.0683 Hom.: 2367

Bravo AF: 0.120

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.63
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6739570; hg19: chr2-49172049;