rs2035545

chr12-57083648-T-Achr12-57083648-T-C

Variant summary

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

The XM_011538056.3(NEMP1):c.271+4166A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,322 control chromosomes in the GnomAD database, including 767 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 0.098 (767 hom., cov: 33)
• Consequence: NEMP1 XM_011538056.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

NEMP1 (HGNC:29001): (nuclear envelope integral membrane protein 1) Involved in nuclear membrane organization. Predicted to be located in nuclear inner membrane. Predicted to be integral component of membrane. Predicted to be active in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEMP1	XM_011538056.3	c.271+4166A>T		intron_variant
NEMP1	XM_011538058.4	c.271+4166A>T		intron_variant
NEMP1	XM_011538060.3	c.271+4166A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEMP1	ENST00000553654.1	n.113+4303A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14875 AN: 152204 Hom.: 768 Cov.: 33

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0977 AC: 14881 AN: 152322 Hom.: 767 Cov.: 33 AF XY: 0.101 AC XY: 7500 AN XY: 74484

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0392 Hom.: 29

Bravo AF: 0.0952

Asia WGS AF: 0.141 AC: 490 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	2.6
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2035545; hg19: chr12-57477431;