rs936232

Variant names:

• chr4-25811448-G-A
• rs936232
• NM_015187.5:c.1564+6690C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

SEL1L3 (HGNC:29108): (SEL1L family member 3) Located in nucleoplasm. [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=-0.9).
• 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 rank	MANE	Protein	UniProt
SEL1L3	NM_015187.5	c.1564+6690C>T		intron_variant	Intron 9 of 23	ENST00000399878.8	NP_056002.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEL1L3	ENST00000399878.8	c.1564+6690C>T		intron_variant	Intron 9 of 23	1	NM_015187.5	ENSP00000382767.3
SEL1L3	ENST00000264868.9	c.1459+6690C>T		intron_variant	Intron 9 of 23	1		ENSP00000264868.5
SEL1L3	ENST00000502949.5	c.1105+6690C>T		intron_variant	Intron 9 of 23	2		ENSP00000425438.1

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

African (AFR) AF: 0.634 AC: 26283 AN: 41442

American (AMR) AF: 0.422 AC: 6454 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1301 AN: 5162

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4818

European-Finnish (FIN) AF: 0.344 AC: 3637 AN: 10564

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24794 AN: 67952

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.390 Hom.: 22413

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
PhyloP100		-1.0
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: rs936232; hg19: chr4-25813070;