chr7-7845903-A-C

Position:

• chr7-7845903-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.157-31378A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,202 control chromosomes in the GnomAD database, including 782 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 0.063 (782 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-31378A>C		intron_variant		ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-31378A>C		intron_variant			NP_001289278.1
UMAD1	NM_001302350.2	c.52-31378A>C		intron_variant			NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-31378A>C		intron_variant			NM_001302348.2	ENSP00000507605	P1

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9508 AN: 152084 Hom.: 773 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0627 AC: 9545 AN: 152202 Hom.: 782 Cov.: 32 AF XY: 0.0648 AC XY: 4821 AN XY: 74410

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.00169

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0255 Hom.: 87

Bravo AF: 0.0714

Asia WGS AF: 0.130 AC: 451 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	13
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6971205; hg19: chr7-7885534;