rs4910907

Variant names:

• chr11-4147621-G-A
• rs4910907
• ENST00000641518.1:n.1093C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-4147621-G-A
• chr11-4147621-G-T

Variant summary

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

The ENST00000641518.1(ENSG00000293433):​n.1093C>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 0.886 in 152,228 control chromosomes in the GnomAD database, including 59,949 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 0.89 (59948 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ENSG00000293433 ENST00000641518.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 5 publications found

Genes affected

ENSG00000293433 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641518.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293433	ENST00000641518.1		n.1093C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000293433	ENST00000641245.1		n.51-284C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134757 AN: 152106 Hom.: 59942 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.884

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.886 AC: 134804 AN: 152224 Hom.: 59948 Cov.: 33 AF XY: 0.881 AC XY: 65576 AN XY: 74414

African (AFR) AF: 0.833 AC: 34575 AN: 41526

American (AMR) AF: 0.856 AC: 13095 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3178 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3888 AN: 5160

South Asian (SAS) AF: 0.933 AC: 4501 AN: 4826

European-Finnish (FIN) AF: 0.885 AC: 9377 AN: 10594

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63349 AN: 68032

Other (OTH) AF: 0.877 AC: 1855 AN: 2116

Alfa AF: 0.919 Hom.: 32870

Bravo AF: 0.877

Asia WGS AF: 0.789 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.40
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4910907; hg19: chr11-4168851;