chr7-7808456-C-T

Position:

• chr7-7808456-C-T

Variant summary

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

The NM_001302348.2(UMAD1):​c.156+6713C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 151,988 control chromosomes in the GnomAD database, including 210 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 0.042 (210 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.156+6713C>T		intron_variant		ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.156+6713C>T		intron_variant			NP_001289278.1
UMAD1	NM_001302350.2	c.51+6713C>T		intron_variant			NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.156+6713C>T		intron_variant			NM_001302348.2	ENSP00000507605	P1

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6428 AN: 151870 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.00878

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0423

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

GnomAD4 genome AF: 0.0423 AC: 6433 AN: 151988 Hom.: 210 Cov.: 32 AF XY: 0.0416 AC XY: 3094 AN XY: 74290

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.0444

Gnomad4 FIN AF: 0.00878

Gnomad4 NFE AF: 0.0182

Gnomad4 OTH AF: 0.0419

Alfa AF: 0.0257 Hom.: 116

Bravo AF: 0.0464

Asia WGS AF: 0.0550 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10237037; hg19: chr7-7848087;