rs16982414

Variant names:

• chr21-28417219-T-A
• rs16982414
• ENST00000657148.1:n.1562-61A>T

Your query was ambiguous. Multiple possible variants found:

• chr21-28417219-T-A
• chr21-28417219-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000657148.1(ENSG00000232855):​n.1562-61A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 0)
• Consequence: ENSG00000232855 ENST00000657148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 1 publications found

Genes affected

ENSG00000232855 (HGNC:58104):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232855	ENST00000657148.1	n.1562-61A>T		intron_variant	Intron 3 of 4
ENSG00000232855	ENST00000824757.1	n.686-61A>T		intron_variant	Intron 5 of 8
ENSG00000232855	ENST00000824758.1	n.1097-61A>T		intron_variant	Intron 8 of 11
ENSG00000232855	ENST00000824759.1	n.768-61A>T		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.70
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs16982414; hg19: chr21-29789540;