rs6979457

Positions:

• chr7-7870237-A-C

Variant summary

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

The NM_001302348.2(UMAD1):​c.157-7044A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,004 control chromosomes in the GnomAD database, including 35,159 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 0.68 (35159 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 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 (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.157-7044A>C		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.157-7044A>C		intron_variant
UMAD1	NM_001302350.2	c.52-7044A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-7044A>C		intron_variant			NM_001302348.2	P1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103074 AN: 151886 Hom.: 35112 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.679 AC: 103171 AN: 152004 Hom.: 35159 Cov.: 32 AF XY: 0.678 AC XY: 50399 AN XY: 74284

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.665

Alfa AF: 0.681 Hom.: 5315

Bravo AF: 0.680

Asia WGS AF: 0.589 AC: 2038 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6979457; hg19: chr7-7909868;