chr5-90523141-CAT-C

Variant names:

• chr5-90523141-CAT-C
• rs2067280
• NM_198273.2:c.255+1892_255+1893delAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_198273.2(LYSMD3):​c.255+1892_255+1893delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,982 control chromosomes in the GnomAD database, including 2,054 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2054 hom., cov: 29)
• Consequence: LYSMD3 NM_198273.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842
• Publications: 2 publications found

Genes affected

LYSMD3 (HGNC:26969): (LysM domain containing 3) Involved in Golgi organization. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYSMD3	NM_198273.2	c.255+1892_255+1893delAT		intron_variant	Intron 2 of 2	ENST00000315948.11	NP_938014.1
LYSMD3	NM_001286812.1	c.255+1892_255+1893delAT		intron_variant	Intron 2 of 2		NP_001273741.1
LYSMD3	XM_047416694.1	c.255+1892_255+1893delAT		intron_variant	Intron 2 of 2		XP_047272650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYSMD3	ENST00000315948.11	c.255+1892_255+1893delAT		intron_variant	Intron 2 of 2	1	NM_198273.2	ENSP00000314518.6
LYSMD3	ENST00000500869.6	c.255+1892_255+1893delAT		intron_variant	Intron 3 of 3	1		ENSP00000427020.1
LYSMD3	ENST00000509384.5	c.255+1892_255+1893delAT		intron_variant	Intron 2 of 2	1		ENSP00000427683.1
LYSMD3	ENST00000453259.2	n.255+1892_255+1893delAT		intron_variant	Intron 2 of 3	3		ENSP00000405507.2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23879 AN: 151864 Hom.: 2050 Cov.: 29

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.157 AC: 23905 AN: 151982 Hom.: 2054 Cov.: 29 AF XY: 0.163 AC XY: 12087 AN XY: 74256

African (AFR) AF: 0.182 AC: 7523 AN: 41438

American (AMR) AF: 0.138 AC: 2112 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1647 AN: 5170

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4826

European-Finnish (FIN) AF: 0.152 AC: 1606 AN: 10552

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8643 AN: 67928

Other (OTH) AF: 0.152 AC: 321 AN: 2106

Alfa AF: 0.139 Hom.: 200

Bravo AF: 0.156

Asia WGS AF: 0.283 AC: 975 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.84
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: rs2067280; hg19: chr5-89818958;