rs73376010

Variant names:

• chr15-34343662-G-A
• rs73376010
• 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. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001284292.2(NUTM1):​c.-35G>A variant causes a 5 prime UTR 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_001284292.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

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	ENST00000537011.6	c.-35G>A		5_prime_UTR_variant	Exon 1 of 8	2	NM_001284292.2	ENSP00000444896.1
NUTM1	ENST00000333756.5	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

African (AFR) AF: 0.00 AC: 0 AN: 31554

American (AMR) AF: 0.00 AC: 0 AN: 35698

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25164

East Asian (EAS) AF: 0.00 AC: 0 AN: 35724

South Asian (SAS) AF: 0.00 AC: 0 AN: 79220

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33456

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5692

European-Non Finnish (NFE) AF: 9.28e-7 AC: 1 AN: 1077806

Other (OTH) AF: 0.00 AC: 0 AN: 57864

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
PhyloP100		-0.13
PromoterAI		-0.028	Neutral

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

Other links and lift over

dbSNP: rs73376010; hg19: chr15-34635863;