rs707457

Variant names:

• chr1-7771004-C-A
• rs707457
• ENST00000772897.1:n.164G>T

Variant summary

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

The ENST00000772897.1(ENSG00000300603):​n.164G>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 0.118 in 152,214 control chromosomes in the GnomAD database, including 1,298 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 0.12 (1298 hom., cov: 32)
• Consequence: ENSG00000300603 ENST00000772897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 13 publications found

Genes affected

ENSG00000300603 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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
ENSG00000300603	ENST00000772897.1	n.164G>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000300603	ENST00000772896.1	n.102+82G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18020 AN: 152096 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0420

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.118 AC: 18024 AN: 152214 Hom.: 1298 Cov.: 32 AF XY: 0.118 AC XY: 8781 AN XY: 74398

African (AFR) AF: 0.0809 AC: 3362 AN: 41552

American (AMR) AF: 0.0810 AC: 1240 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3468

East Asian (EAS) AF: 0.0515 AC: 266 AN: 5162

South Asian (SAS) AF: 0.0420 AC: 203 AN: 4830

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10251 AN: 68000

Other (OTH) AF: 0.0986 AC: 208 AN: 2110

Alfa AF: 0.125 Hom.: 2009

Bravo AF: 0.108

Asia WGS AF: 0.0560 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		0.13
PromoterAI		-0.038	Neutral

Splicing

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

Other links and lift over

dbSNP: rs707457; hg19: chr1-7831064;