rs17444393

Positions:

• chr9-70034948-T-C

Variant summary

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

The XR_007061571.1(LOC124902179):​n.89-749A>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 0.208 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: LOC124902179 XR_007061571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

LOC124902179 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902179	XR_007061571.1	n.89-749A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAMDC2-AS1	ENST00000628563.2	n.199-749A>G		intron_variant, non_coding_transcript_variant		5
MAMDC2-AS1	ENST00000629922.2	n.300-749A>G		intron_variant, non_coding_transcript_variant		5
MAMDC2-AS1	ENST00000630191.2	n.396-749A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.221

Alfa AF: 0.202 Hom.: 2608

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17444393; hg19: chr9-72649864;