rs726871

Variant names:

• chr2-168655881-A-G
• rs726871
• NM_203463.3:c.465+24839A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-168655881-A-G
• chr2-168655881-A-T

Variant summary

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

The NM_203463.3(CERS6):​c.465+24839A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 152,336 control chromosomes in the GnomAD database, including 105 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 0.017 (105 hom., cov: 32)
• Consequence: CERS6 NM_203463.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

Genes affected

CERS6 (HGNC:23826): (ceramide synthase 6) Enables sphingosine N-acyltransferase activity. Involved in ceramide biosynthetic process. Located 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CERS6	NM_203463.3	c.465+24839A>G		intron_variant	Intron 4 of 9	ENST00000305747.11	NP_982288.1
CERS6	NM_001256126.2	c.465+24839A>G		intron_variant	Intron 4 of 10		NP_001243055.1
CERS6	XM_005246440.6	c.-112+11560A>G		intron_variant	Intron 1 of 7		XP_005246497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CERS6	ENST00000305747.11	c.465+24839A>G		intron_variant	Intron 4 of 9	2	NM_203463.3	ENSP00000306579.6
CERS6	ENST00000392687.4	c.465+24839A>G		intron_variant	Intron 4 of 10	1		ENSP00000376453.4

Frequencies

GnomAD3 genomes AF: 0.0171 AC: 2605 AN: 152218 Hom.: 105 Cov.: 32

Gnomad AFR AF: 0.00318

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00892

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0171 AC: 2602 AN: 152336 Hom.: 105 Cov.: 32 AF XY: 0.0192 AC XY: 1428 AN XY: 74482

African (AFR) AF: 0.00317 AC: 132 AN: 41580

American (AMR) AF: 0.0494 AC: 756 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00950 AC: 33 AN: 3472

East Asian (EAS) AF: 0.156 AC: 810 AN: 5180

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4828

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00892 AC: 607 AN: 68026

Other (OTH) AF: 0.0151 AC: 32 AN: 2116

Alfa AF: 0.0102 Hom.: 1

Bravo AF: 0.0195

Asia WGS AF: 0.0710 AC: 246 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	3.4
DANN	Benign	0.77
PhyloP100		0.35
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: rs726871; hg19: chr2-169512391;