chr7-7734210-T-C

Variant names:

• chr7-7734210-T-C
• rs17136898
• NM_001302348.2:c.82+60757T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302348.2(UMAD1):​c.82+60757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,070 control chromosomes in the GnomAD database, including 1,357 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 0.13 (1357 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 6 publications found

Genes affected

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

ENSG00000283549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.82+60757T>C		intron_variant	Intron 2 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.82+60757T>C		intron_variant	Intron 2 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.-24+58002T>C		intron_variant	Intron 3 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.82+60757T>C		intron_variant	Intron 2 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20362 AN: 151950 Hom.: 1354 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.134 AC: 20397 AN: 152070 Hom.: 1357 Cov.: 31 AF XY: 0.133 AC XY: 9854 AN XY: 74370

African (AFR) AF: 0.155 AC: 6418 AN: 41490

American (AMR) AF: 0.102 AC: 1561 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3460

East Asian (EAS) AF: 0.0966 AC: 501 AN: 5188

South Asian (SAS) AF: 0.159 AC: 767 AN: 4822

European-Finnish (FIN) AF: 0.0942 AC: 996 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8953 AN: 67946

Other (OTH) AF: 0.156 AC: 329 AN: 2110

Alfa AF: 0.135 Hom.: 2812

Bravo AF: 0.135

Asia WGS AF: 0.163 AC: 567 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	1.8
DANN	Benign	0.41
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs17136898; hg19: chr7-7773841;