chr7-69372016-C-T

Variant names:

• chr7-69372016-C-T
• rs3105377
• ENST00000421513.1:n.273-12554G>A

Variant summary

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

The ENST00000421513.1(ENSG00000225718):​n.273-12554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,002 control chromosomes in the GnomAD database, including 21,708 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 0.52 (21708 hom., cov: 33)
• Consequence: ENSG00000225718 ENST00000421513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 4 publications found

Genes affected

ENSG00000225718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421513.1. 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
	ENSG00000225718	ENST00000421513.1	TSL:3	n.273-12554G>A		intron	N/A
	ENSG00000225718	ENST00000435148.1	TSL:3	n.156+58752G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79160 AN: 151884 Hom.: 21697 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.521 AC: 79190 AN: 152002 Hom.: 21708 Cov.: 33 AF XY: 0.515 AC XY: 38291 AN XY: 74296

African (AFR) AF: 0.361 AC: 14985 AN: 41468

American (AMR) AF: 0.476 AC: 7274 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1503 AN: 5162

South Asian (SAS) AF: 0.475 AC: 2284 AN: 4808

European-Finnish (FIN) AF: 0.604 AC: 6369 AN: 10544

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42932 AN: 67960

Other (OTH) AF: 0.509 AC: 1075 AN: 2112

Alfa AF: 0.570 Hom.: 4268

Bravo AF: 0.505

Asia WGS AF: 0.418 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.25
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs3105377; hg19: chr7-68837002;