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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370420	XR_001750686.2	n.63+8306C>A		intron_variant	Intron 1 of 3
LOC105370420	XR_943662.3	n.66-6395C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4307HG	ENST00000552303.1	n.268+8306C>A		intron_variant	Intron 2 of 5	4
NOVA1-DT	ENST00000656336.1	n.481-48364C>A		intron_variant	Intron 2 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs6575421; hg19: chr14-27554812;