chr16-67486220-A-T

Position:

• chr16-67486220-A-T

Variant summary

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

The NR_184227.1(ATP6V0D1-DT):​n.345+1892A>T variant causes a intron, non coding transcript 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: 27)
• Consequence: ATP6V0D1-DT NR_184227.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

ATP6V0D1-DT (HGNC:55268): (ATP6V0D1 divergent transcript)

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=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6V0D1-DT	NR_184227.1	n.345+1892A>T		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	NR_184225.1	n.345+1892A>T		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	NR_184226.1	n.345+1892A>T		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	NR_184228.1	n.549+1688A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6V0D1-DT	ENST00000656196.1	n.425+1892A>T		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	ENST00000602476.1	n.88-594A>T		intron_variant, non_coding_transcript_variant		3
ATP6V0D1-DT	ENST00000635000.1	n.332+1892A>T		intron_variant, non_coding_transcript_variant		5
ATP6V0D1-DT	ENST00000659360.1	n.366+1892A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 27

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

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13338499; hg19: chr16-67520123;