rs6938239

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-34715858-G-A
• chr6-34715858-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP6V1FP1		n.34715858G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP6V1FP1	ENST00000334441.4	n.246G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000299678	ENST00000765567.1	n.155-2676C>T		intron_variant	Intron 2 of 2
ENSG00000299678	ENST00000765568.1	n.134-2676C>T		intron_variant	Intron 2 of 3

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 v4.3

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;