rs721608

Variant names:

• chr11-57230449-A-G
• rs721608
• ENST00000777433.1:n.173T>C

Variant summary

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

The ENST00000777433.1(ENSG00000301258):​n.173T>C 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 0.285 in 152,050 control chromosomes in the GnomAD database, including 6,757 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 0.29 (6757 hom., cov: 31)
• Consequence: ENSG00000301258 ENST00000777433.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 12 publications found

Genes affected

ENSG00000301258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369309	XR_001748217.1	n.244-228T>C		intron_variant	Intron 1 of 4
LOC105369309	XR_007062670.1	n.244-228T>C		intron_variant	Intron 1 of 6
LOC105369309	XR_007062671.1	n.244-228T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301258	ENST00000777433.1	n.173T>C		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43334 AN: 151932 Hom.: 6760 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.285 AC: 43340 AN: 152050 Hom.: 6757 Cov.: 31 AF XY: 0.279 AC XY: 20709 AN XY: 74310

African (AFR) AF: 0.160 AC: 6652 AN: 41478

American (AMR) AF: 0.269 AC: 4117 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3470

East Asian (EAS) AF: 0.188 AC: 967 AN: 5142

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2936 AN: 10580

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25279 AN: 67944

Other (OTH) AF: 0.276 AC: 583 AN: 2114

Alfa AF: 0.348 Hom.: 4998

Bravo AF: 0.279

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.43
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs721608; hg19: chr11-56997923;