chr6-34715858-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000334441.4(ATP6V1FP1):​n.246G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.845 in 170,734 control chromosomes in the GnomAD database, including 61,209 homozygotes. 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: 𝑓 0.84 (53804 hom., cov: 30)
  • Exomes 𝑓: 0.89 (7405 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

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>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299678	ENST00000765567.1		n.155-2676C>T		intron	N/A
	ENSG00000299678	ENST00000765568.1		n.134-2676C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127613 AN: 151924 Hom.: 53764 Cov.: 30

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.848

GnomAD4 exome AF: 0.888 AC: 16591 AN: 18692 Hom.: 7405 Cov.: 0 AF XY: 0.892 AC XY: 9293 AN XY: 10420

African (AFR) AF: 0.856 AC: 440 AN: 514

American (AMR) AF: 0.954 AC: 1042 AN: 1092

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 95 AN: 106

East Asian (EAS) AF: 0.992 AC: 962 AN: 970

South Asian (SAS) AF: 0.946 AC: 1544 AN: 1632

European-Finnish (FIN) AF: 0.813 AC: 3674 AN: 4518

Middle Eastern (MID) AF: 0.894 AC: 1477 AN: 1652

European-Non Finnish (NFE) AF: 0.896 AC: 6543 AN: 7302

Other (OTH) AF: 0.898 AC: 814 AN: 906

GnomAD4 genome AF: 0.840 AC: 127711 AN: 152042 Hom.: 53804 Cov.: 30 AF XY: 0.839 AC XY: 62339 AN XY: 74318

African (AFR) AF: 0.794 AC: 32899 AN: 41436

American (AMR) AF: 0.881 AC: 13459 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2886 AN: 3470

East Asian (EAS) AF: 0.989 AC: 5113 AN: 5172

South Asian (SAS) AF: 0.921 AC: 4434 AN: 4816

European-Finnish (FIN) AF: 0.784 AC: 8301 AN: 10584

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57823 AN: 67976

Other (OTH) AF: 0.849 AC: 1792 AN: 2110

Alfa AF: 0.849 Hom.: 89396

Bravo AF: 0.844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.3
DANN	Benign	0.67
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;