11-128622844-T-C

Variant names:

• chr11-128622844-T-C
• rs4937362
• ENST00000835144.1:n.415T>C

Variant summary

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

The ENST00000835144.1(ENSG00000308574):​n.415T>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 0.485 in 152,152 control chromosomes in the GnomAD database, including 18,422 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 0.49 (18422 hom., cov: 33)
• Consequence: ENSG00000308574 ENST00000835144.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 32 publications found

Genes affected

ENSG00000308574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835144.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308574	ENST00000835144.1		n.415T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000245008	ENST00000602773.2	TSL:6	n.208-2070A>G		intron	N/A
	ENSG00000245008	ENST00000647054.1		n.596-2070A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73783 AN: 152034 Hom.: 18416 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.485 AC: 73821 AN: 152152 Hom.: 18422 Cov.: 33 AF XY: 0.488 AC XY: 36327 AN XY: 74396

African (AFR) AF: 0.374 AC: 15494 AN: 41472

American (AMR) AF: 0.488 AC: 7472 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1527 AN: 3466

East Asian (EAS) AF: 0.360 AC: 1861 AN: 5166

South Asian (SAS) AF: 0.486 AC: 2345 AN: 4826

European-Finnish (FIN) AF: 0.599 AC: 6350 AN: 10608

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 37019 AN: 67998

Other (OTH) AF: 0.485 AC: 1025 AN: 2114

Alfa AF: 0.520 Hom.: 87788

Bravo AF: 0.472

Asia WGS AF: 0.446 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.34
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4937362; hg19: chr11-128492739;