chr7-128206960-A-G

Position:

• chr7-128206960-A-G

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.720A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,166 control chromosomes in the GnomAD database, including 8,761 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 0.32 (8761 hom., cov: 33)
• Consequence: ENST00000710955.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901744	XR_007060516.1	n.665A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000710955.1	n.720A>G		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48881 AN: 152048 Hom.: 8764 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.321 AC: 48885 AN: 152166 Hom.: 8761 Cov.: 33 AF XY: 0.324 AC XY: 24086 AN XY: 74384

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.335

Alfa AF: 0.350 Hom.: 9994

Bravo AF: 0.312

Asia WGS AF: 0.472 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11772985; hg19: chr7-127847013;