rs2335462

Variant names:

• chr16-2884316-T-A
• rs2335462
• NM_138439.3:c.-200+950T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-2884316-T-A
• chr16-2884316-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138439.3(FLYWCH2):​c.-200+950T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
• Consequence: FLYWCH2 NM_138439.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

FLYWCH2 (HGNC:25178): (FLYWCH family member 2) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLYWCH2	NM_138439.3	c.-200+950T>A		intron_variant	Intron 1 of 3	ENST00000396958.8	NP_612448.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLYWCH2	ENST00000396958.8	c.-200+950T>A		intron_variant	Intron 1 of 3	1	NM_138439.3	ENSP00000380159.3
FLYWCH2	ENST00000572006.1	c.-200+950T>A		intron_variant	Intron 1 of 2	2		ENSP00000459223.1
FLYWCH2	ENST00000293981.10	c.-200+1044T>A		intron_variant	Intron 1 of 3	3		ENSP00000293981.6
FLYWCH2	ENST00000573965.1	c.-99+950T>A		intron_variant	Intron 1 of 1	2		ENSP00000461275.1

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.2
DANN	Benign	0.75

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: rs2335462; hg19: chr16-2934317;