rs77585961

Variant names:

• chr1-9151409-C-T
• rs77585961
• ENST00000635687.1:n.813G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000635687.1(MIR34AHG):​n.813G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 340,962 control chromosomes in the GnomAD database, including 274 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 0.033 (109 hom., cov: 32)
  • Exomes 𝑓: 0.035 (165 hom.)
• Consequence: MIR34AHG ENST00000635687.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 1 publications found

Genes affected

MIR34AHG (HGNC:51913): (MIR34A host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0331 (5039/152322) while in subpopulation NFE AF = 0.0483 (3288/68022). AF 95% confidence interval is 0.047. There are 109 homozygotes in GnomAd4. There are 2411 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR34AHG	NR_132742.1	n.759G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR34AHG	ENST00000635687.1	n.813G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
MIR34AHG	ENST00000782879.1	n.464-11388G>A		intron_variant	Intron 2 of 2
MIR34AHG	ENST00000782880.1	n.339-11388G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5042 AN: 152204 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.00924

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0351

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0416

GnomAD4 exome AF: 0.0351 AC: 6626 AN: 188640 Hom.: 165 Cov.: 0 AF XY: 0.0322 AC XY: 3347 AN XY: 103954

African (AFR) AF: 0.00782 AC: 38 AN: 4862

American (AMR) AF: 0.0397 AC: 339 AN: 8532

Ashkenazi Jewish (ASJ) AF: 0.0286 AC: 124 AN: 4336

East Asian (EAS) AF: 0.000275 AC: 2 AN: 7284

South Asian (SAS) AF: 0.0120 AC: 444 AN: 37042

European-Finnish (FIN) AF: 0.0398 AC: 356 AN: 8940

Middle Eastern (MID) AF: 0.0562 AC: 37 AN: 658

European-Non Finnish (NFE) AF: 0.0460 AC: 4964 AN: 107826

Other (OTH) AF: 0.0352 AC: 322 AN: 9160

GnomAD4 genome AF: 0.0331 AC: 5039 AN: 152322 Hom.: 109 Cov.: 32 AF XY: 0.0324 AC XY: 2411 AN XY: 74498

African (AFR) AF: 0.00921 AC: 383 AN: 41576

American (AMR) AF: 0.0452 AC: 691 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4832

European-Finnish (FIN) AF: 0.0351 AC: 373 AN: 10622

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0483 AC: 3288 AN: 68022

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0398 Hom.: 103

Bravo AF: 0.0331

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.51
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs77585961; hg19: chr1-9211468;