rs6575421

Variant names:

• chr14-27085606-C-A
• rs6575421
• ENST00000552303.1:n.268+8306C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-27085606-C-A
• chr14-27085606-C-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552303.1(MIR4307HG):​n.268+8306C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,862 control chromosomes in the GnomAD database, including 17,547 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 (17547 hom., cov: 32)
• Consequence: MIR4307HG ENST00000552303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82
• Publications: 2 publications found

Genes affected

MIR4307HG (HGNC:52004): (MIR4307 host gene)

NOVA1-DT (HGNC:19827): (NOVA1 divergent transcript)

LOC105370420 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552303.1. 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
	MIR4307HG	ENST00000552303.1	TSL:4	n.268+8306C>A		intron	N/A
	NOVA1-DT	ENST00000656336.1		n.481-48364C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72299 AN: 151742 Hom.: 17536 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.476 AC: 72343 AN: 151862 Hom.: 17547 Cov.: 32 AF XY: 0.478 AC XY: 35484 AN XY: 74208

African (AFR) AF: 0.464 AC: 19228 AN: 41418

American (AMR) AF: 0.542 AC: 8248 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1064 AN: 5138

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5686 AN: 10546

Middle Eastern (MID) AF: 0.566 AC: 164 AN: 290

European-Non Finnish (NFE) AF: 0.476 AC: 32312 AN: 67942

Other (OTH) AF: 0.477 AC: 1006 AN: 2110

Alfa AF: 0.474 Hom.: 29290

Bravo AF: 0.474

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		2.8

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: rs6575421;

hg19: chr14-27554812;