6-34715858-G-C

Variant names:

• chr6-34715858-G-C
• rs6938239
• ENST00000334441.4:n.246G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000334441.4(ATP6V1FP1):​n.246G>C variant causes a non coding transcript exon change. 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: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATP6V1FP1 ENST00000334441.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.14
• Publications: 32 publications found

Genes affected

ATP6V1FP1 (HGNC:56922):

ENSG00000299678 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000334441.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP6V1FP1	ENST00000334441.4	TSL:6	n.246G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299678	ENST00000765567.1		n.155-2676C>G		intron	N/A
	ENSG00000299678	ENST00000765568.1		n.134-2676C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 18720 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10438

African (AFR) AF: 0.00 AC: 0 AN: 514

American (AMR) AF: 0.00 AC: 0 AN: 1094

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 106

East Asian (EAS) AF: 0.00 AC: 0 AN: 970

South Asian (SAS) AF: 0.00 AC: 0 AN: 1632

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4530

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1652

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 7316

Other (OTH) AF: 0.00 AC: 0 AN: 906

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs6938239; hg19: chr6-34683635;