rs11723705

Variant names:

• chr4-54884905-T-C
• rs11723705
• ENST00000848199.1:n.416-7433A>G

Variant summary

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

The ENST00000848199.1(ENSG00000310211):​n.416-7433A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,190 control chromosomes in the GnomAD database, including 51,553 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 0.82 (51553 hom., cov: 32)
• Consequence: ENSG00000310211 ENST00000848199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 2 publications found

Genes affected

ENSG00000310211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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
ENSG00000310211	ENST00000848199.1	n.416-7433A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124891 AN: 152072 Hom.: 51502 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.821 AC: 125002 AN: 152190 Hom.: 51553 Cov.: 32 AF XY: 0.826 AC XY: 61444 AN XY: 74406

African (AFR) AF: 0.870 AC: 36138 AN: 41534

American (AMR) AF: 0.858 AC: 13120 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4832 AN: 5158

South Asian (SAS) AF: 0.875 AC: 4214 AN: 4816

European-Finnish (FIN) AF: 0.845 AC: 8955 AN: 10594

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52523 AN: 68000

Other (OTH) AF: 0.803 AC: 1698 AN: 2114

Alfa AF: 0.789 Hom.: 26091

Bravo AF: 0.825

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11723705; hg19: chr4-55751071;