rs7222705

Variant names:

• chr17-65438071-C-A
• rs7222705
• ENST00000778874.1:n.1698G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-65438071-C-A
• chr17-65438071-C-T

Variant summary

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

The ENST00000778874.1(ENSG00000301434):​n.1698G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,020 control chromosomes in the GnomAD database, including 7,296 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 0.24 (7296 hom., cov: 32)
• Consequence: ENSG00000301434 ENST00000778874.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 3 publications found

Genes affected

ENSG00000301434 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

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
ENSG00000301434	ENST00000778874.1	n.1698G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301434	ENST00000778875.1	n.1404G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301434	ENST00000778872.1	n.452+36293G>T		intron_variant	Intron 1 of 1
ENSG00000301434	ENST00000778873.1	n.30+18820G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35946 AN: 151902 Hom.: 7274 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.237 AC: 36012 AN: 152020 Hom.: 7296 Cov.: 32 AF XY: 0.234 AC XY: 17372 AN XY: 74332

African (AFR) AF: 0.553 AC: 22882 AN: 41414

American (AMR) AF: 0.136 AC: 2073 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1637 AN: 5162

South Asian (SAS) AF: 0.123 AC: 592 AN: 4816

European-Finnish (FIN) AF: 0.121 AC: 1284 AN: 10574

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0972 AC: 6611 AN: 67980

Other (OTH) AF: 0.216 AC: 457 AN: 2114

Alfa AF: 0.115 Hom.: 1275

Bravo AF: 0.254

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.43
DANN	Benign	0.45
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7222705; hg19: chr17-63434189;