7-49550951-T-C

Variant names:

• chr7-49550951-T-C
• rs2107699
• ENST00000664348.2:n.223+26616T>C

Variant summary

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

The ENST00000664348.2(ENSG00000286995):​n.223+26616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,060 control chromosomes in the GnomAD database, including 8,597 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 (8597 hom., cov: 32)
• Consequence: ENSG00000286995 ENST00000664348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 1 publications found

Genes affected

ENSG00000286995 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664348.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286995	ENST00000664348.2		n.223+26616T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47914 AN: 151942 Hom.: 8587 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.315 AC: 47960 AN: 152060 Hom.: 8597 Cov.: 32 AF XY: 0.323 AC XY: 24016 AN XY: 74318

African (AFR) AF: 0.154 AC: 6387 AN: 41528

American (AMR) AF: 0.345 AC: 5258 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3064 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4628 AN: 10570

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24259 AN: 67942

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.261 Hom.: 997

Bravo AF: 0.303

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.29
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs2107699; hg19: chr7-49590547;