2-149840634-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110240.1(MMADHC-DT):n.536-7275A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,066 control chromosomes in the GnomAD database, including 41,261 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 0.73 (41261 hom., cov: 32)
• Consequence: MMADHC-DT NR_110240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

Genes affected

MMADHC-DT (HGNC:41087): (MMADHC divergent transcript)

LINC01931 (HGNC:52743): (long intergenic non-protein coding RNA 1931)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMADHC-DT	NR_110240.1	n.536-7275A>G		intron_variant, non_coding_transcript_variant
LINC01931	NR_145421.1	n.1302+16817T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.244-7275A>G		intron_variant, non_coding_transcript_variant
LINC01931	ENST00000658047.1	n.937+16817T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111448 AN: 151948 Hom.: 41234 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.733 AC: 111525 AN: 152066 Hom.: 41261 Cov.: 32 AF XY: 0.730 AC XY: 54251 AN XY: 74326

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.725

Alfa AF: 0.777 Hom.: 70204

Bravo AF: 0.719

Asia WGS AF: 0.729 AC: 2530 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.30
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11889862; hg19: chr2-150697148;