chr7-7739460-G-T

Position:

• chr7-7739460-G-T

Variant summary

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

The NM_001302348.2(UMAD1):​c.83-62210G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,064 control chromosomes in the GnomAD database, including 7,363 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 0.29 (7363 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.83-62210G>T		intron_variant		ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.83-62210G>T		intron_variant			NP_001289278.1
UMAD1	NM_001302350.2	c.-23-62210G>T		intron_variant			NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.83-62210G>T		intron_variant			NM_001302348.2	ENSP00000507605	P1
	ENST00000418534.3	n.601-476C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44268 AN: 151944 Hom.: 7348 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.291 AC: 44321 AN: 152064 Hom.: 7363 Cov.: 33 AF XY: 0.287 AC XY: 21336 AN XY: 74330

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.286

Alfa AF: 0.241 Hom.: 5349

Bravo AF: 0.301

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13237260; hg19: chr7-7779091;