rs7578654

Variant names:

• chr2-49283034-A-C
• rs7578654
• ENST00000634588.1:n.493-125168A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-49283034-A-C
• chr2-49283034-A-G
• chr2-49283034-A-T

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.493-125168A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 494,086 control chromosomes in the GnomAD database, including 45,741 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 0.45 (15268 hom., cov: 33)
  • Exomes 𝑓: 0.42 (30473 hom.)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 7 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=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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.493-125168A>C		intron	N/A
	ENSG00000282998	ENST00000635306.2	TSL:5	n.407+48840T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67935 AN: 151536 Hom.: 15245 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.437

GnomAD2 exomes AF: 0.419 AC: 91900 AN: 219402 AF XY: 0.419

Gnomad AFR exome AF: 0.481

Gnomad AMR exome AF: 0.381

Gnomad ASJ exome AF: 0.396

Gnomad EAS exome AF: 0.376

Gnomad FIN exome AF: 0.424

Gnomad NFE exome AF: 0.437

Gnomad OTH exome AF: 0.401

GnomAD4 exome AF: 0.417 AC: 142816 AN: 342432 Hom.: 30473 Cov.: 0 AF XY: 0.417 AC XY: 82541 AN XY: 197834

African (AFR) AF: 0.477 AC: 4557 AN: 9550

American (AMR) AF: 0.378 AC: 13103 AN: 34642

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 4323 AN: 10996

East Asian (EAS) AF: 0.369 AC: 4554 AN: 12350

South Asian (SAS) AF: 0.403 AC: 25084 AN: 62238

European-Finnish (FIN) AF: 0.421 AC: 6663 AN: 15844

Middle Eastern (MID) AF: 0.334 AC: 915 AN: 2742

European-Non Finnish (NFE) AF: 0.432 AC: 77259 AN: 178654

Other (OTH) AF: 0.412 AC: 6358 AN: 15416

GnomAD4 genome AF: 0.448 AC: 68010 AN: 151654 Hom.: 15268 Cov.: 33 AF XY: 0.447 AC XY: 33095 AN XY: 74102

African (AFR) AF: 0.488 AC: 20178 AN: 41390

American (AMR) AF: 0.390 AC: 5928 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1410 AN: 3466

East Asian (EAS) AF: 0.391 AC: 1997 AN: 5104

South Asian (SAS) AF: 0.425 AC: 2045 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4654 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30379 AN: 67788

Other (OTH) AF: 0.436 AC: 920 AN: 2108

Alfa AF: 0.441 Hom.: 49002

Bravo AF: 0.446

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.3
DANN	Benign	0.69
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7578654; hg19: chr2-49510173;