rs6720394

Variant names:

• chr2-111231795-T-G
• rs6720394
• ENST00000439362.6:n.656+1833A>C

Variant summary

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

The ENST00000439362.6(MIR4435-2HG):​n.656+1833A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,148 control chromosomes in the GnomAD database, including 959 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 (959 hom., cov: 32)
• Consequence: MIR4435-2HG ENST00000439362.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 17 publications found

Genes affected

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

LOC124907867 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4435-2HG	NR_015395.2	n.2776+1833A>C		intron_variant	Intron 5 of 6
MIR4435-2HG	NR_136161.1	n.749+1833A>C		intron_variant	Intron 5 of 5
MIR4435-2HG	NR_136162.1	n.2581+1833A>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4435-2HG	ENST00000439362.6	n.656+1833A>C		intron_variant	Intron 5 of 5	1
MIR4435-2HG	ENST00000443467.6	n.960+1833A>C		intron_variant	Intron 7 of 8	3
MIR4435-2HG	ENST00000451884.6	n.1306+1833A>C		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16305 AN: 152030 Hom.: 959 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.107 AC: 16310 AN: 152148 Hom.: 959 Cov.: 32 AF XY: 0.104 AC XY: 7733 AN XY: 74374

African (AFR) AF: 0.124 AC: 5166 AN: 41502

American (AMR) AF: 0.0750 AC: 1146 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.0363 AC: 175 AN: 4820

European-Finnish (FIN) AF: 0.112 AC: 1181 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7988 AN: 67998

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.111 Hom.: 3830

Bravo AF: 0.106

Asia WGS AF: 0.0300 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6720394; hg19: chr2-111989372;