rs936232

chr4-25811448-G-A

Variant summary

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

The NM_015187.5(SEL1L3):c.1564+6690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,000 control chromosomes in the GnomAD database, including 15,909 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 0.44 (15909 hom., cov: 32)
• Consequence: SEL1L3 NM_015187.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

SEL1L3 (HGNC:29108): (SEL1L family member 3) Located in nucleoplasm. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEL1L3	NM_015187.5	c.1564+6690C>T		intron_variant		ENST00000399878.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEL1L3	ENST00000399878.8	c.1564+6690C>T		intron_variant		1	NM_015187.5	P1
SEL1L3	ENST00000264868.9	c.1459+6690C>T		intron_variant		1
SEL1L3	ENST00000502949.5	c.1105+6690C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66560 AN: 151882 Hom.: 15861 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.439 AC: 66669 AN: 152000 Hom.: 15909 Cov.: 32 AF XY: 0.435 AC XY: 32285 AN XY: 74296

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.409

Alfa AF: 0.380 Hom.: 15180

Bravo AF: 0.453

Asia WGS AF: 0.329 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.24
Dann	Benign	0.54

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

LitVar

Other links and lift over

dbSNP: rs936232; hg19: chr4-25813070;