rs520046

Variant names:

• chr6-122446048-G-A
• rs520046
• NM_020755.4:c.1226+726C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-122446048-G-A
• chr6-122446048-G-C

Variant summary

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

The NM_020755.4(SERINC1):​c.1226+726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,612 control chromosomes in the GnomAD database, including 37,498 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 0.70 (37498 hom., cov: 31)
• Consequence: SERINC1 NM_020755.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 3 publications found

Genes affected

SERINC1 (HGNC:13464): (serine incorporator 1) Predicted to enable protein-macromolecule adaptor activity. Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Predicted to be located in endoplasmic reticulum membrane and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERINC1	NM_020755.4	c.1226+726C>T		intron_variant	Intron 9 of 9	ENST00000339697.5	NP_065806.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERINC1	ENST00000339697.5	c.1226+726C>T		intron_variant	Intron 9 of 9	1	NM_020755.4	ENSP00000342962.3

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106380 AN: 151492 Hom.: 37464 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.702 AC: 106469 AN: 151612 Hom.: 37498 Cov.: 31 AF XY: 0.701 AC XY: 51913 AN XY: 74094

African (AFR) AF: 0.686 AC: 28314 AN: 41300

American (AMR) AF: 0.740 AC: 11267 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2598 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3732 AN: 5178

South Asian (SAS) AF: 0.777 AC: 3732 AN: 4802

European-Finnish (FIN) AF: 0.649 AC: 6765 AN: 10428

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47699 AN: 67892

Other (OTH) AF: 0.699 AC: 1473 AN: 2108

Alfa AF: 0.619 Hom.: 2102

Bravo AF: 0.706

Asia WGS AF: 0.741 AC: 2573 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
DANN	Benign	0.46
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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: rs520046; hg19: chr6-122767193;