rs211804

Variant names:

• chr7-110451403-A-C
• rs211804
• ENST00000843038.1:n.487T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-110451403-A-C
• chr7-110451403-A-G
• chr7-110451403-A-T

Variant summary

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

The ENST00000843038.1(ENSG00000226965):​n.487T>G 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 0.878 in 152,114 control chromosomes in the GnomAD database, including 58,777 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 0.88 (58777 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000843038.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 1 publications found

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375450	XR_927862.3	n.392-5023A>C		intron_variant	Intron 2 of 2
LOC105375451	XR_927863.3	n.291-18497T>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226965	ENST00000843038.1	n.487T>G		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000226965	ENST00000435466.2	n.328-18497T>G		intron_variant	Intron 3 of 4	4
ENSG00000226965	ENST00000657059.1	n.438-18497T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133449 AN: 151996 Hom.: 58730 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.878 AC: 133557 AN: 152114 Hom.: 58777 Cov.: 32 AF XY: 0.881 AC XY: 65493 AN XY: 74354

African (AFR) AF: 0.929 AC: 38542 AN: 41486

American (AMR) AF: 0.872 AC: 13306 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2768 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4880 AN: 5178

South Asian (SAS) AF: 0.875 AC: 4212 AN: 4816

European-Finnish (FIN) AF: 0.904 AC: 9582 AN: 10594

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57372 AN: 67986

Other (OTH) AF: 0.869 AC: 1836 AN: 2112

Alfa AF: 0.849 Hom.: 23174

Bravo AF: 0.878

Asia WGS AF: 0.898 AC: 3119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs211804; hg19: chr7-110091460;