chr7-9963989-C-T

Variant names:

• chr7-9963989-C-T
• rs17162294
• ENST00000451755.2:n.284+2566C>T

Variant summary

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

The ENST00000451755.2(ENSG00000235431):​n.284+2566C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152,128 control chromosomes in the GnomAD database, including 974 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 0.099 (974 hom., cov: 33)
• Consequence: ENSG00000235431 ENST00000451755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 2 publications found

Genes affected

ENSG00000235431 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451755.2. 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
	LOC105375146	NR_187855.1		n.355+2566C>T		intron	N/A
	LOC105375146	NR_187856.1		n.355+2566C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235431	ENST00000451755.2	TSL:3	n.284+2566C>T		intron	N/A
	ENSG00000235431	ENST00000663710.1		n.200+2566C>T		intron	N/A
	ENSG00000235431	ENST00000671028.1		n.281+2566C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15029 AN: 152012 Hom.: 966 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0990 AC: 15065 AN: 152128 Hom.: 974 Cov.: 33 AF XY: 0.102 AC XY: 7592 AN XY: 74376

African (AFR) AF: 0.133 AC: 5520 AN: 41520

American (AMR) AF: 0.118 AC: 1800 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1586 AN: 5162

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4816

European-Finnish (FIN) AF: 0.0977 AC: 1034 AN: 10582

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4178 AN: 67992

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

Alfa AF: 0.0739 Hom.: 2544

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.0
DANN	Benign	0.69
PhyloP100		0.38

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: rs17162294;

hg19: chr7-10003616;