rs73376010

Variant names:

• chr15-34343662-G-A
• NM_001284292.2:c.-35G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-34343662-G-A
• chr15-34343662-G-C
• chr15-34343662-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001284293.2(NUTM1):​c.30G>A​(p.Lys10Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000723 in 1,382,178 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: NUTM1 NM_001284293.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

Genes affected

NUTM1 (HGNC:29919): (NUT midline carcinoma family member 1) Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP7: Synonymous conserved (PhyloP=-0.134 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM1	NM_001284292.2	c.-35G>A		5_prime_UTR_variant	Exon 1 of 8	ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2	c.30G>A	p.Lys10Lys	synonymous_variant	Exon 1 of 7		NP_001271222.2
NUTM1	NM_175741.3	c.-204G>A		5_prime_UTR_variant	Exon 1 of 8		NP_786883.2
NUTM1	XM_047432341.1	c.-207G>A		5_prime_UTR_variant	Exon 1 of 8		XP_047288297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM1	ENST00000537011	c.-35G>A		5_prime_UTR_variant	Exon 1 of 8	2	NM_001284292.2	ENSP00000444896.1
NUTM1	ENST00000333756	c.-204G>A		5_prime_UTR_variant	Exon 1 of 8	1		ENSP00000329448.4
NUTM1	ENST00000438749.7	c.30G>A	p.Lys10Lys	synonymous_variant	Exon 1 of 7	2		ENSP00000407031.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.23e-7 AC: 1 AN: 1382178 Hom.: 0 Cov.: 29 AF XY: 0.00000147 AC XY: 1 AN XY: 682078

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.28e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.0
DANN	Benign	0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-34635863;