chr7-110443615-A-G

Position:

• chr7-110443615-A-G

Variant summary

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

The ENST00000667232.1(ENSG00000226965):​n.316-10709T>C 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 0.882 in 152,036 control chromosomes in the GnomAD database, including 59,218 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 0.88 (59218 hom., cov: 29)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375450	XR_927862.3	n.391+163A>G		intron_variant, non_coding_transcript_variant
LOC105375451	XR_927863.3	n.291-10709T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667232.1	n.316-10709T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.882 AC: 133980 AN: 151918 Hom.: 59174 Cov.: 29

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.882 AC: 134085 AN: 152036 Hom.: 59218 Cov.: 29 AF XY: 0.884 AC XY: 65669 AN XY: 74292

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.879

Alfa AF: 0.878 Hom.: 6842

Bravo AF: 0.882

Asia WGS AF: 0.898 AC: 3120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211811; hg19: chr7-110083672;