chr7-116259281-T-A

Position:

• chr7-116259281-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444244.1(ENSG00000243243):​n.66-4046A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,696 control chromosomes in the GnomAD database, including 15,148 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 0.44 (15148 hom., cov: 30)
• Consequence: ENST00000444244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000444244.1	n.66-4046A>T		intron_variant, non_coding_transcript_variant		3
	ENST00000446355.2	n.204-15345A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67328 AN: 151586 Hom.: 15134 Cov.: 30

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.444 AC: 67390 AN: 151696 Hom.: 15148 Cov.: 30 AF XY: 0.448 AC XY: 33204 AN XY: 74130

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.429

Alfa AF: 0.429 Hom.: 1785

Bravo AF: 0.450

Asia WGS AF: 0.538 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4730721; hg19: chr7-115899335;