rs719530

chr7-110250908-T-C

Variant summary

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

The ENST00000667232.1(ENSG00000226965):n.487-69898A>G 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 0.585 in 151,908 control chromosomes in the GnomAD database, including 26,419 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 0.58 (26419 hom., cov: 32)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667232.1	n.487-69898A>G		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.406-69898A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88790 AN: 151790 Hom.: 26387 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.585 AC: 88864 AN: 151908 Hom.: 26419 Cov.: 32 AF XY: 0.578 AC XY: 42938 AN XY: 74272

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.578

Alfa AF: 0.564 Hom.: 23299

Bravo AF: 0.606

Asia WGS AF: 0.507 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.0
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719530; hg19: chr7-109890965;