6-122451758-C-CAAAAAAA

Position:

• chr6-122451758-C-CAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_020755.4(SERINC1):​c.760-11_760-5dupTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 18)
  • Exomes 𝑓: 0.0012 (2 hom.)
• Consequence: SERINC1 NM_020755.4 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.875

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

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 6-122451758-C-CAAAAAAA is Benign according to our data. Variant chr6-122451758-C-CAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 2656894.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERINC1	NM_020755.4	c.760-11_760-5dupTTTTTTT		splice_region_variant, intron_variant		ENST00000339697.5	NP_065806.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERINC1	ENST00000339697.5	c.760-11_760-5dupTTTTTTT		splice_region_variant, intron_variant		1	NM_020755.4	ENSP00000342962.3

Frequencies

GnomAD3 genomes AF: 0.000107 AC: 3 AN: 28144 Hom.: 0 Cov.: 18

Gnomad AFR AF: 0.000271

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000634

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00121 AC: 73 AN: 60274 Hom.: 2 Cov.: 4 AF XY: 0.00124 AC XY: 44 AN XY: 35386

Gnomad4 AFR exome AF: 0.000642

Gnomad4 AMR exome AF: 0.000685

Gnomad4 ASJ exome AF: 0.000903

Gnomad4 EAS exome AF: 0.000373

Gnomad4 SAS exome AF: 0.00159

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00145

Gnomad4 OTH exome AF: 0.000986

GnomAD4 genome AF: 0.000107 AC: 3 AN: 28152 Hom.: 0 Cov.: 18 AF XY: 0.0000806 AC XY: 1 AN XY: 12410

Gnomad4 AFR AF: 0.000271

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000634

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2022

SERINC1: BP4 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750920534; hg19: chr6-122772903;