rs17444393

Variant names:

• chr9-70034948-T-C
• rs17444393
• ENST00000628563.2:n.199-749A>G

Variant summary

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

The ENST00000628563.2(MAMDC2-AS1):​n.199-749A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,166 control chromosomes in the GnomAD database, including 3,348 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 0.21 (3348 hom., cov: 32)
• Consequence: MAMDC2-AS1 ENST00000628563.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 6 publications found

Genes affected

MAMDC2-AS1 (HGNC:48719): (MAMDC2 antisense RNA 1)

LOC124902179 (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 (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902179	XR_007061571.1	n.89-749A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAMDC2-AS1	ENST00000628563.2	n.199-749A>G		intron_variant	Intron 2 of 2	5
MAMDC2-AS1	ENST00000629922.2	n.300-749A>G		intron_variant	Intron 3 of 3	5
MAMDC2-AS1	ENST00000630191.2	n.396-749A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31564 AN: 152048 Hom.: 3333 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.208 AC: 31601 AN: 152166 Hom.: 3348 Cov.: 32 AF XY: 0.210 AC XY: 15617 AN XY: 74390

African (AFR) AF: 0.212 AC: 8784 AN: 41502

American (AMR) AF: 0.271 AC: 4143 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3472

East Asian (EAS) AF: 0.155 AC: 799 AN: 5166

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4810

European-Finnish (FIN) AF: 0.195 AC: 2069 AN: 10602

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12950 AN: 68006

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.203 Hom.: 4359

Bravo AF: 0.212

Asia WGS AF: 0.205 AC: 715 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	0.92
DANN	Benign	0.44
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs17444393; hg19: chr9-72649864;