rs978770

Variant names:

• chr11-111017868-C-T
• rs978770
• ENST00000660486.1:n.50+4367C>T

Variant summary

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

The ENST00000660486.1(ENSG00000287556):​n.50+4367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,586 control chromosomes in the GnomAD database, including 11,306 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 0.37 (11306 hom., cov: 32)
• Consequence: ENSG00000287556 ENST00000660486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 2 publications found

Genes affected

ENSG00000287556 (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 (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660486.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287556	ENST00000660486.1		n.50+4367C>T		intron	N/A
	ENSG00000299094	ENST00000760419.1		n.384+604G>A		intron	N/A
	ENSG00000299094	ENST00000760420.1		n.582+604G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56783 AN: 151466 Hom.: 11289 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.375 AC: 56842 AN: 151586 Hom.: 11306 Cov.: 32 AF XY: 0.385 AC XY: 28481 AN XY: 74038

African (AFR) AF: 0.390 AC: 16099 AN: 41300

American (AMR) AF: 0.394 AC: 6004 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1439 AN: 3462

East Asian (EAS) AF: 0.785 AC: 4005 AN: 5104

South Asian (SAS) AF: 0.657 AC: 3161 AN: 4812

European-Finnish (FIN) AF: 0.325 AC: 3407 AN: 10498

Middle Eastern (MID) AF: 0.490 AC: 141 AN: 288

European-Non Finnish (NFE) AF: 0.317 AC: 21539 AN: 67858

Other (OTH) AF: 0.387 AC: 815 AN: 2108

Alfa AF: 0.347 Hom.: 5211

Bravo AF: 0.379

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.60

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs978770;

hg19: chr11-110888592;